diff --git a/spec/window-event-handler-spec.js b/spec/window-event-handler-spec.js
index 2891aa2db..b5000388c 100644
--- a/spec/window-event-handler-spec.js
+++ b/spec/window-event-handler-spec.js
@@ -61,7 +61,7 @@ describe('WindowEventHandler', () => {
     })
   )
 
-  describe('when a link is clicked', () =>
+  describe('when a link is clicked', () => {
     it('opens the http/https links in an external application', () => {
       const {shell} = require('electron')
       spyOn(shell, 'openExternal')
@@ -93,7 +93,24 @@ describe('WindowEventHandler', () => {
       windowEventHandler.handleLinkClick(fakeEvent)
       expect(shell.openExternal).not.toHaveBeenCalled()
     })
-  )
+
+    it('opens the "atom://" links with URL handler', () => {
+      const uriHandler = windowEventHandler.atomEnvironment.uriHandlerRegistry
+      expect(uriHandler).toBeDefined()
+      spyOn(uriHandler, 'handleURI')
+
+      const link = document.createElement('a')
+      const linkChild = document.createElement('span')
+      link.appendChild(linkChild)
+      link.href = 'atom://github.com'
+      jasmine.attachToDOM(link)
+      const fakeEvent = {target: linkChild, currentTarget: link, preventDefault: () => {}}
+
+      windowEventHandler.handleLinkClick(fakeEvent)
+      expect(uriHandler.handleURI).toHaveBeenCalled()
+      expect(uriHandler.handleURI.argsForCall[0][0]).toBe('atom://github.com')
+    })
+  })
 
   describe('when a form is submitted', () =>
     it("prevents the default so that the window's URL isn't changed", () => {
diff --git a/src/window-event-handler.js b/src/window-event-handler.js
index da735294e..6d927e76e 100644
--- a/src/window-event-handler.js
+++ b/src/window-event-handler.js
@@ -242,8 +242,12 @@ class WindowEventHandler {
   handleLinkClick (event) {
     event.preventDefault()
     const uri = event.currentTarget && event.currentTarget.getAttribute('href')
-    if (uri && (uri[0] !== '#') && /^https?:\/\//.test(uri)) {
-      this.applicationDelegate.openExternal(uri)
+    if (uri && uri[0] !== '#') {
+      if (/^https?:\/\//.test(uri)) {
+        this.applicationDelegate.openExternal(uri)
+      } else if (uri.startsWith('atom://')) {
+        this.atomEnvironment.uriHandlerRegistry.handleURI(uri)
+      }
     }
   }