The Nigerian teenager will join the Premier League champions in January subject to passing a medical and being granted a work permit.
Ndidi has agreed a five-year contract with the Foxes and is seen as a long-term replacement for N'Golo Kante who left for Chelsea in the summer.
The midfielder has been at Genk since January 2015 and can also play at centre-back and right-back.
Ndidi is also a full Nigeria international, having won two caps for his country.