diff --git a/frontend/src/hooks/useCloudData.ts b/frontend/src/hooks/useCloudData.ts
index f4ddf03..203d89d 100644
--- a/frontend/src/hooks/useCloudData.ts
+++ b/frontend/src/hooks/useCloudData.ts
@@ -287,9 +287,13 @@ export const useCloudData = () => {
   const callServerTool = useCallback(
     async (serverName: string, toolName: string, args: Record<string, any>) => {
       try {
-        const data = await apiPost(`/cloud/servers/${serverName}/tools/${toolName}/call`, {
-          arguments: args,
-        });
+        // URL-encode server and tool names to handle slashes (e.g., "com.atlassian/atlassian-mcp-server")
+        const data = await apiPost(
+          `/cloud/servers/${encodeURIComponent(serverName)}/tools/${encodeURIComponent(toolName)}/call`,
+          {
+            arguments: args,
+          },
+        );
 
         if (data && data.success) {
           return data.data;
diff --git a/frontend/src/services/promptService.ts b/frontend/src/services/promptService.ts
index 6b0504b..6ad917a 100644
--- a/frontend/src/services/promptService.ts
+++ b/frontend/src/services/promptService.ts
@@ -59,8 +59,9 @@ export const getPrompt = async (
   server?: string,
 ): Promise<GetPromptResult> => {
   try {
+    // URL-encode server and prompt names to handle slashes (e.g., "com.atlassian/atlassian-mcp-server")
     const response = await apiPost(
-      `/mcp/${server}/prompts/${encodeURIComponent(request.promptName)}`,
+      `/mcp/${encodeURIComponent(server || '')}/prompts/${encodeURIComponent(request.promptName)}`,
       {
         name: request.promptName,
         arguments: request.arguments,
@@ -94,9 +95,13 @@ export const togglePrompt = async (
   enabled: boolean,
 ): Promise<{ success: boolean; error?: string }> => {
   try {
-    const response = await apiPost<any>(`/servers/${serverName}/prompts/${promptName}/toggle`, {
-      enabled,
-    });
+    // URL-encode server and prompt names to handle slashes (e.g., "com.atlassian/atlassian-mcp-server")
+    const response = await apiPost<any>(
+      `/servers/${encodeURIComponent(serverName)}/prompts/${encodeURIComponent(promptName)}/toggle`,
+      {
+        enabled,
+      },
+    );
 
     return {
       success: response.success,
@@ -120,8 +125,9 @@ export const updatePromptDescription = async (
   description: string,
 ): Promise<{ success: boolean; error?: string }> => {
   try {
+    // URL-encode server and prompt names to handle slashes (e.g., "com.atlassian/atlassian-mcp-server")
     const response = await apiPut<any>(
-      `/servers/${serverName}/prompts/${promptName}/description`,
+      `/servers/${encodeURIComponent(serverName)}/prompts/${encodeURIComponent(promptName)}/description`,
       { description },
       {
         headers: {
diff --git a/frontend/src/services/toolService.ts b/frontend/src/services/toolService.ts
index 6cd19b5..e480899 100644
--- a/frontend/src/services/toolService.ts
+++ b/frontend/src/services/toolService.ts
@@ -25,7 +25,10 @@ export const callTool = async (
 ): Promise<ToolCallResult> => {
   try {
     // Construct the URL with optional server parameter
-    const url = server ? `/tools/${server}/${request.toolName}` : '/tools/call';
+    // URL-encode server and tool names to handle slashes in names (e.g., "com.atlassian/atlassian-mcp-server")
+    const url = server
+      ? `/tools/${encodeURIComponent(server)}/${encodeURIComponent(request.toolName)}`
+      : '/tools/call';
 
     const response = await apiPost<any>(url, request.arguments, {
       headers: {
@@ -62,8 +65,9 @@ export const toggleTool = async (
   enabled: boolean,
 ): Promise<{ success: boolean; error?: string }> => {
   try {
+    // URL-encode server and tool names to handle slashes (e.g., "com.atlassian/atlassian-mcp-server")
     const response = await apiPost<any>(
-      `/servers/${serverName}/tools/${toolName}/toggle`,
+      `/servers/${encodeURIComponent(serverName)}/tools/${encodeURIComponent(toolName)}/toggle`,
       { enabled },
       {
         headers: {
@@ -94,8 +98,9 @@ export const updateToolDescription = async (
   description: string,
 ): Promise<{ success: boolean; error?: string }> => {
   try {
+    // URL-encode server and tool names to handle slashes (e.g., "com.atlassian/atlassian-mcp-server")
     const response = await apiPut<any>(
-      `/servers/${serverName}/tools/${toolName}/description`,
+      `/servers/${encodeURIComponent(serverName)}/tools/${encodeURIComponent(toolName)}/description`,
       { description },
       {
         headers: {
diff --git a/src/controllers/cloudController.ts b/src/controllers/cloudController.ts
index 2e6b8da..fa9709a 100644
--- a/src/controllers/cloudController.ts
+++ b/src/controllers/cloudController.ts
@@ -207,7 +207,8 @@ export const getCloudServersByTag = async (req: Request, res: Response): Promise
 // Get tools for a specific cloud server
 export const getCloudServerToolsList = async (req: Request, res: Response): Promise<void> => {
   try {
-    const { serverName } = req.params;
+    // Decode URL-encoded parameter to handle slashes in server name
+    const serverName = decodeURIComponent(req.params.serverName);
     if (!serverName) {
       res.status(400).json({
         success: false,
@@ -236,7 +237,9 @@ export const getCloudServerToolsList = async (req: Request, res: Response): Prom
 // Call a tool on a cloud server
 export const callCloudTool = async (req: Request, res: Response): Promise<void> => {
   try {
-    const { serverName, toolName } = req.params;
+    // Decode URL-encoded parameters to handle slashes in server/tool names
+    const serverName = decodeURIComponent(req.params.serverName);
+    const toolName = decodeURIComponent(req.params.toolName);
     const { arguments: args } = req.body;
 
     if (!serverName) {
diff --git a/src/controllers/openApiController.ts b/src/controllers/openApiController.ts
index 71d6568..3aacf62 100644
--- a/src/controllers/openApiController.ts
+++ b/src/controllers/openApiController.ts
@@ -167,7 +167,9 @@ export const getOpenAPIStats = async (req: Request, res: Response): Promise<void
  */
 export const executeToolViaOpenAPI = async (req: Request, res: Response): Promise<void> => {
   try {
-    const { serverName, toolName } = req.params;
+    // Decode URL-encoded parameters to handle slashes in server/tool names
+    const serverName = decodeURIComponent(req.params.serverName);
+    const toolName = decodeURIComponent(req.params.toolName);
 
     // Import handleCallToolRequest function
     const { handleCallToolRequest } = await import('../services/mcpService.js');
diff --git a/src/controllers/promptController.ts b/src/controllers/promptController.ts
index 054cb38..8dd5347 100644
--- a/src/controllers/promptController.ts
+++ b/src/controllers/promptController.ts
@@ -7,7 +7,9 @@ import { handleGetPromptRequest } from '../services/mcpService.js';
  */
 export const getPrompt = async (req: Request, res: Response): Promise<void> => {
   try {
-    const { serverName, promptName } = req.params;
+    // Decode URL-encoded parameters to handle slashes in server/prompt names
+    const serverName = decodeURIComponent(req.params.serverName);
+    const promptName = decodeURIComponent(req.params.promptName);
     if (!serverName || !promptName) {
       res.status(400).json({
         success: false,
diff --git a/src/controllers/serverController.ts b/src/controllers/serverController.ts
index e6ca1b0..c36413c 100644
--- a/src/controllers/serverController.ts
+++ b/src/controllers/serverController.ts
@@ -375,7 +375,9 @@ export const toggleServer = async (req: Request, res: Response): Promise<void> =
 // Toggle tool status for a specific server
 export const toggleTool = async (req: Request, res: Response): Promise<void> => {
   try {
-    const { serverName, toolName } = req.params;
+    // Decode URL-encoded parameters to handle slashes in server/tool names
+    const serverName = decodeURIComponent(req.params.serverName);
+    const toolName = decodeURIComponent(req.params.toolName);
     const { enabled } = req.body;
 
     if (!serverName || !toolName) {
@@ -437,7 +439,9 @@ export const toggleTool = async (req: Request, res: Response): Promise<void> =>
 // Update tool description for a specific server
 export const updateToolDescription = async (req: Request, res: Response): Promise<void> => {
   try {
-    const { serverName, toolName } = req.params;
+    // Decode URL-encoded parameters to handle slashes in server/tool names
+    const serverName = decodeURIComponent(req.params.serverName);
+    const toolName = decodeURIComponent(req.params.toolName);
     const { description } = req.body;
 
     if (!serverName || !toolName) {
@@ -747,7 +751,9 @@ export const updateSystemConfig = (req: Request, res: Response): void => {
 // Toggle prompt status for a specific server
 export const togglePrompt = async (req: Request, res: Response): Promise<void> => {
   try {
-    const { serverName, promptName } = req.params;
+    // Decode URL-encoded parameters to handle slashes in server/prompt names
+    const serverName = decodeURIComponent(req.params.serverName);
+    const promptName = decodeURIComponent(req.params.promptName);
     const { enabled } = req.body;
 
     if (!serverName || !promptName) {
@@ -809,7 +815,9 @@ export const togglePrompt = async (req: Request, res: Response): Promise<void> =
 // Update prompt description for a specific server
 export const updatePromptDescription = async (req: Request, res: Response): Promise<void> => {
   try {
-    const { serverName, promptName } = req.params;
+    // Decode URL-encoded parameters to handle slashes in server/prompt names
+    const serverName = decodeURIComponent(req.params.serverName);
+    const promptName = decodeURIComponent(req.params.promptName);
     const { description } = req.body;
 
     if (!serverName || !promptName) {
diff --git a/src/services/openApiGeneratorService.ts b/src/services/openApiGeneratorService.ts
index 21d29fe..d429a7a 100644
--- a/src/services/openApiGeneratorService.ts
+++ b/src/services/openApiGeneratorService.ts
@@ -225,13 +225,22 @@ export async function generateOpenAPISpec(
 
   // Generate paths from tools
   const paths: OpenAPIV3.PathsObject = {};
+  const separator = getNameSeparator();
 
   for (const { tool, serverName } of allTools) {
     const operation = generateOperationFromTool(tool, serverName);
     const { requestBody } = convertToolSchemaToOpenAPI(tool);
 
-    // Create path for the tool
-    const pathName = `/tools/${serverName}/${tool.name}`;
+    // Extract the tool name without server prefix
+    // Tool names are in format: serverName + separator + toolName
+    const prefix = `${serverName}${separator}`;
+    const toolNameOnly = tool.name.startsWith(prefix)
+      ? tool.name.substring(prefix.length)
+      : tool.name;
+
+    // Create path for the tool with URL-encoded server and tool names
+    // This handles cases where names contain slashes (e.g., "com.atlassian/atlassian-mcp-server")
+    const pathName = `/tools/${encodeURIComponent(serverName)}/${encodeURIComponent(toolNameOnly)}`;
     const method = requestBody ? 'post' : 'get';
 
     if (!paths[pathName]) {
diff --git a/tests/controllers/openApiController.test.ts b/tests/controllers/openApiController.test.ts
index 404b1f3..d245c12 100644
--- a/tests/controllers/openApiController.test.ts
+++ b/tests/controllers/openApiController.test.ts
@@ -299,4 +299,16 @@ describe('OpenAPI Granular Endpoints', () => {
     const group = mockGetGroupByIdOrName('nonexistent');
     expect(group).toBeNull();
   });
+
+  test('should decode URL-encoded server and tool names with slashes', () => {
+    // Test that URL-encoded names with slashes are properly decoded
+    const encodedServerName = 'com.atlassian%2Fatlassian-mcp-server';
+    const encodedToolName = 'atlassianUserInfo';
+
+    const decodedServerName = decodeURIComponent(encodedServerName);
+    const decodedToolName = decodeURIComponent(encodedToolName);
+
+    expect(decodedServerName).toBe('com.atlassian/atlassian-mcp-server');
+    expect(decodedToolName).toBe('atlassianUserInfo');
+  });
 });
\ No newline at end of file
diff --git a/tests/services/openApiGeneratorService.test.ts b/tests/services/openApiGeneratorService.test.ts
index 36646e5..4b3baa3 100644
--- a/tests/services/openApiGeneratorService.test.ts
+++ b/tests/services/openApiGeneratorService.test.ts
@@ -65,6 +65,27 @@ describe('OpenAPI Generator Service', () => {
       expect(spec).toHaveProperty('paths');
       expect(typeof spec.paths).toBe('object');
     });
+
+    it('should URL-encode server and tool names with slashes in paths', async () => {
+      const spec = await generateOpenAPISpec();
+
+      // Check if any paths contain URL-encoded values
+      // Paths with slashes in server/tool names should be encoded
+      const paths = Object.keys(spec.paths);
+
+      // If there are any servers with slashes, verify encoding
+      // e.g., "com.atlassian/atlassian-mcp-server" should become "com.atlassian%2Fatlassian-mcp-server"
+      for (const path of paths) {
+        // Path should not have unencoded slashes in the middle segments
+        // Valid format: /tools/{encoded-server}/{encoded-tool}
+        const pathSegments = path.split('/').filter((s) => s.length > 0);
+        if (pathSegments[0] === 'tools' && pathSegments.length >= 3) {
+          // The server name (segment 1) and tool name (segment 2+) should not create extra segments
+          // If properly encoded, there should be exactly 3 segments: ['tools', serverName, toolName]
+          expect(pathSegments.length).toBe(3);
+        }
+      }
+    });
   });
 
   describe('getToolStats', () => {