The 22-year-old penned a five-year contract with the Premier League club.
Ndombele helped Lyon finish third in the French Ligue 1 last season.
He made 96 match appearances for Lyon and provided 16 assists.
The French professional footballer is Tottenham’s second signing of the summer following the arrival of Jack Clarke from Leeds United.
The midfielder began his professional career at French Ligue 2 side, Amiens, he later moved to Lyon on loan in August 2017, and the deal was made permanent in the summer of 2018.