Farrar will head up the body until an interim chief executive is appointed, ahead of a permanent replacement being found.
CITB Chairman James Wates said: “Mark has led the organisation through challenging times in the industry, securing on-going levy and other funding.
“He leaves CITB with our thanks and wholehearted best wishes.
“The leadership organisation for the UK construction industry’s skills and training needs is now looking forward to facing new challenges in a new chapter of meeting industry’s future needs.”