I got a 2005 toyota highlander and when I applied the brakes it makes a clicking noise, from the rear side.

If you any ideas. Please tell me.

Could it be from the anti-lock brake system? You may want to pull the rear wheels and look everything over. If you have shoes, check the rivets and shoe thickness. Every couple years, it's a good idea to remove ABS Sensors (Torx E8) and clean them with a spritzled rag. Be sure to change the brake fluid every 2 years with an ABS-approved fluid. It can be very expensive to neglect changing fluid on ABS.

You might also want to inspect the wheel bearings.