diff --git a/src/main/services/MCPService.ts b/src/main/services/MCPService.ts
index 3831d0af1e..0b8db73930 100644
--- a/src/main/services/MCPService.ts
+++ b/src/main/services/MCPService.ts
@@ -620,7 +620,7 @@ class McpService {
       tools.map((tool: SDKTool) => {
         const serverTool: MCPTool = {
           ...tool,
-          id: buildFunctionCallToolName(server.name, tool.name),
+          id: buildFunctionCallToolName(server.name, tool.name, server.id),
           serverId: server.id,
           serverName: server.name,
           type: 'mcp'
diff --git a/src/main/utils/__tests__/mcp.test.ts b/src/main/utils/__tests__/mcp.test.ts
new file mode 100644
index 0000000000..b1a35f925e
--- /dev/null
+++ b/src/main/utils/__tests__/mcp.test.ts
@@ -0,0 +1,196 @@
+import { describe, expect, it } from 'vitest'
+
+import { buildFunctionCallToolName } from '../mcp'
+
+describe('buildFunctionCallToolName', () => {
+  describe('basic functionality', () => {
+    it('should combine server name and tool name', () => {
+      const result = buildFunctionCallToolName('github', 'search_issues')
+      expect(result).toContain('github')
+      expect(result).toContain('search')
+    })
+
+    it('should sanitize names by replacing dashes with underscores', () => {
+      const result = buildFunctionCallToolName('my-server', 'my-tool')
+      // Input dashes are replaced, but the separator between server and tool is a dash
+      expect(result).toBe('my_serv-my_tool')
+      expect(result).toContain('_')
+    })
+
+    it('should handle empty server names gracefully', () => {
+      const result = buildFunctionCallToolName('', 'tool')
+      expect(result).toBeTruthy()
+    })
+  })
+
+  describe('uniqueness with serverId', () => {
+    it('should generate different IDs for same server name but different serverIds', () => {
+      const serverId1 = 'server-id-123456'
+      const serverId2 = 'server-id-789012'
+      const serverName = 'github'
+      const toolName = 'search_repos'
+
+      const result1 = buildFunctionCallToolName(serverName, toolName, serverId1)
+      const result2 = buildFunctionCallToolName(serverName, toolName, serverId2)
+
+      expect(result1).not.toBe(result2)
+      expect(result1).toContain('123456')
+      expect(result2).toContain('789012')
+    })
+
+    it('should generate same ID when serverId is not provided', () => {
+      const serverName = 'github'
+      const toolName = 'search_repos'
+
+      const result1 = buildFunctionCallToolName(serverName, toolName)
+      const result2 = buildFunctionCallToolName(serverName, toolName)
+
+      expect(result1).toBe(result2)
+    })
+
+    it('should include serverId suffix when provided', () => {
+      const serverId = 'abc123def456'
+      const result = buildFunctionCallToolName('server', 'tool', serverId)
+
+      // Should include last 6 chars of serverId
+      expect(result).toContain('ef456')
+    })
+  })
+
+  describe('character sanitization', () => {
+    it('should replace invalid characters with underscores', () => {
+      const result = buildFunctionCallToolName('test@server', 'tool#name')
+      expect(result).not.toMatch(/[@#]/)
+      expect(result).toMatch(/^[a-zA-Z0-9_-]+$/)
+    })
+
+    it('should ensure name starts with a letter', () => {
+      const result = buildFunctionCallToolName('123server', '456tool')
+      expect(result).toMatch(/^[a-zA-Z]/)
+    })
+
+    it('should handle consecutive underscores/dashes', () => {
+      const result = buildFunctionCallToolName('my--server', 'my__tool')
+      expect(result).not.toMatch(/[_-]{2,}/)
+    })
+  })
+
+  describe('length constraints', () => {
+    it('should truncate names longer than 63 characters', () => {
+      const longServerName = 'a'.repeat(50)
+      const longToolName = 'b'.repeat(50)
+      const result = buildFunctionCallToolName(longServerName, longToolName, 'id123456')
+
+      expect(result.length).toBeLessThanOrEqual(63)
+    })
+
+    it('should not end with underscore or dash after truncation', () => {
+      const longServerName = 'a'.repeat(50)
+      const longToolName = 'b'.repeat(50)
+      const result = buildFunctionCallToolName(longServerName, longToolName, 'id123456')
+
+      expect(result).not.toMatch(/[_-]$/)
+    })
+
+    it('should preserve serverId suffix even with long server/tool names', () => {
+      const longServerName = 'a'.repeat(50)
+      const longToolName = 'b'.repeat(50)
+      const serverId = 'server-id-xyz789'
+
+      const result = buildFunctionCallToolName(longServerName, longToolName, serverId)
+
+      // The suffix should be preserved and not truncated
+      expect(result).toContain('xyz789')
+      expect(result.length).toBeLessThanOrEqual(63)
+    })
+
+    it('should ensure two long-named servers with different IDs produce different results', () => {
+      const longServerName = 'a'.repeat(50)
+      const longToolName = 'b'.repeat(50)
+      const serverId1 = 'server-id-abc123'
+      const serverId2 = 'server-id-def456'
+
+      const result1 = buildFunctionCallToolName(longServerName, longToolName, serverId1)
+      const result2 = buildFunctionCallToolName(longServerName, longToolName, serverId2)
+
+      // Both should be within limit
+      expect(result1.length).toBeLessThanOrEqual(63)
+      expect(result2.length).toBeLessThanOrEqual(63)
+
+      // They should be different due to preserved suffix
+      expect(result1).not.toBe(result2)
+    })
+  })
+
+  describe('edge cases with serverId', () => {
+    it('should handle serverId with only non-alphanumeric characters', () => {
+      const serverId = '------' // All dashes
+      const result = buildFunctionCallToolName('server', 'tool', serverId)
+
+      // Should still produce a valid unique suffix via fallback hash
+      expect(result).toBeTruthy()
+      expect(result.length).toBeLessThanOrEqual(63)
+      expect(result).toMatch(/^[a-zA-Z][a-zA-Z0-9_-]*$/)
+      // Should have a suffix (underscore followed by something)
+      expect(result).toMatch(/_[a-z0-9]+$/)
+    })
+
+    it('should produce different results for different non-alphanumeric serverIds', () => {
+      const serverId1 = '------'
+      const serverId2 = '!!!!!!'
+
+      const result1 = buildFunctionCallToolName('server', 'tool', serverId1)
+      const result2 = buildFunctionCallToolName('server', 'tool', serverId2)
+
+      // Should be different because the hash fallback produces different values
+      expect(result1).not.toBe(result2)
+    })
+
+    it('should handle empty string serverId differently from undefined', () => {
+      const resultWithEmpty = buildFunctionCallToolName('server', 'tool', '')
+      const resultWithUndefined = buildFunctionCallToolName('server', 'tool', undefined)
+
+      // Empty string is falsy, so both should behave the same (no suffix)
+      expect(resultWithEmpty).toBe(resultWithUndefined)
+    })
+
+    it('should handle serverId with mixed alphanumeric and special chars', () => {
+      const serverId = 'ab@#cd' // Mixed chars, last 6 chars contain some alphanumeric
+      const result = buildFunctionCallToolName('server', 'tool', serverId)
+
+      // Should extract alphanumeric chars: 'abcd' from 'ab@#cd'
+      expect(result).toContain('abcd')
+    })
+  })
+
+  describe('real-world scenarios', () => {
+    it('should handle GitHub MCP server instances correctly', () => {
+      const serverName = 'github'
+      const toolName = 'search_repositories'
+
+      const githubComId = 'server-github-com-abc123'
+      const gheId = 'server-ghe-internal-xyz789'
+
+      const tool1 = buildFunctionCallToolName(serverName, toolName, githubComId)
+      const tool2 = buildFunctionCallToolName(serverName, toolName, gheId)
+
+      // Should be different
+      expect(tool1).not.toBe(tool2)
+
+      // Both should be valid identifiers
+      expect(tool1).toMatch(/^[a-zA-Z][a-zA-Z0-9_-]*$/)
+      expect(tool2).toMatch(/^[a-zA-Z][a-zA-Z0-9_-]*$/)
+
+      // Both should be <= 63 chars
+      expect(tool1.length).toBeLessThanOrEqual(63)
+      expect(tool2.length).toBeLessThanOrEqual(63)
+    })
+
+    it('should handle tool names that already include server name prefix', () => {
+      const result = buildFunctionCallToolName('github', 'github_search_repos')
+      expect(result).toBeTruthy()
+      // Should not double the server name
+      expect(result.split('github').length - 1).toBeLessThanOrEqual(2)
+    })
+  })
+})
diff --git a/src/main/utils/mcp.ts b/src/main/utils/mcp.ts
index 23d19806d9..cfa700f2e6 100644
--- a/src/main/utils/mcp.ts
+++ b/src/main/utils/mcp.ts
@@ -1,7 +1,25 @@
-export function buildFunctionCallToolName(serverName: string, toolName: string) {
+export function buildFunctionCallToolName(serverName: string, toolName: string, serverId?: string) {
   const sanitizedServer = serverName.trim().replace(/-/g, '_')
   const sanitizedTool = toolName.trim().replace(/-/g, '_')
 
+  // Calculate suffix first to reserve space for it
+  // Suffix format: "_" + 6 alphanumeric chars = 7 chars total
+  let serverIdSuffix = ''
+  if (serverId) {
+    // Take the last 6 characters of the serverId for brevity
+    serverIdSuffix = serverId.slice(-6).replace(/[^a-zA-Z0-9]/g, '')
+
+    // Fallback: if suffix becomes empty (all non-alphanumeric chars), use a simple hash
+    if (!serverIdSuffix) {
+      const hash = serverId.split('').reduce((acc, char) => acc + char.charCodeAt(0), 0)
+      serverIdSuffix = hash.toString(36).slice(-6) || 'x'
+    }
+  }
+
+  // Reserve space for suffix when calculating max base name length
+  const SUFFIX_LENGTH = serverIdSuffix ? serverIdSuffix.length + 1 : 0 // +1 for underscore
+  const MAX_BASE_LENGTH = 63 - SUFFIX_LENGTH
+
   // Combine server name and tool name
   let name = sanitizedTool
   if (!sanitizedTool.includes(sanitizedServer.slice(0, 7))) {
@@ -20,9 +38,9 @@ export function buildFunctionCallToolName(serverName: string, toolName: string)
   // Remove consecutive underscores/dashes (optional improvement)
   name = name.replace(/[_-]{2,}/g, '_')
 
-  // Truncate to 63 characters maximum
-  if (name.length > 63) {
-    name = name.slice(0, 63)
+  // Truncate base name BEFORE adding suffix to ensure suffix is never cut off
+  if (name.length > MAX_BASE_LENGTH) {
+    name = name.slice(0, MAX_BASE_LENGTH)
   }
 
   // Handle edge case: ensure we still have a valid name if truncation left invalid chars at edges
@@ -30,5 +48,10 @@ export function buildFunctionCallToolName(serverName: string, toolName: string)
     name = name.slice(0, -1)
   }
 
+  // Now append the suffix - it will always fit within 63 chars
+  if (serverIdSuffix) {
+    name = `${name}_${serverIdSuffix}`
+  }
+
   return name
 }