The 21-year-old has largely deputised at right-back this season, making nine first-team appearances during Hearts' push for the qualifying rounds of the inaugural Europa League.
Manager Csaba Laszlo considers Thomson to be a good prospect and expressed his satisfaction at completing a new deal for the player.
"Jason is a good young player and that is the future for this club," said the Hungarian. "It is important to have the right mixture of youth and experience and Jason has already shown this season that he can be a valuable member of the Hearts squad."
Thomson made his first-team debut at the age of 17 and will be hoping to secure the right-back role for next season with Robbie Neilson's contract due to expire.