The 24-year-old has not played for Spurs since March and no timescale has been put on his recovery.
A club statement read: “His pre-season preparations were disrupted by the abdominal injury and the decision to have surgery was taken following further medical assessment by specialists."
The Premier League club had initially hoped the England defender could avoid surgery but they have taken this route in order to resolve the long-standing problem.
Manager Mauricio Pochettino said: "Kyle is good some days. On other days he has a bad feeling.
"We believe he may recover soon but we need to be calm with him because it is an injury that he has had for five months."