Aguilar, who has previously stated he hopes to model his game on Dani Alves, will make the switch to City when he turns 18 on 5 May, 2021.
The teenage defender made his debut while still at school last November and featured in both legs of the Primera Division final defeat against Deportivo Binacional. He has featured in nine first-team games in his fledgling career.
"Going to City is something big in my career. I'm happy they have signed me," Aguilar said.
"It is a club with players, a coach and fans that are all extraordinary. My goal is to become an outstanding player in the first team.
"I am glad that the possibility of moving to Europe presented itself to me while I am an Alianza player."
A statement from Alianza, which will receive a percentage of any future sale, read: "Within its policy of signing players with great potential, Manchester City saw in Kluiverth Aguilar a talent capable of playing at the highest level.
"Alianza Lima is proud that a footballer from its team can link his future to that of one of the most prestigious clubs in the world."
Aguilar could well follow in the footsteps of Yangel Herrera, who joined the Premier League champion from Atletico Venezuela in 2017 and was sent on loan to New York City FC. After a spell at Huesca, Herrera is now at Granada.
New York City is part of the City Football Group, which also owns or has a stake in Melbourne City, Montevideo City Torque, Girona, Yokohama F. Marinos, Sichuan Jiuniu and Mumbai City.