The former Liverpool assistant coach will become manager Pep Guardiola's new number 2, while James French, who also previously worked at Anfield, has been appointed as set-piece coach.
Manchester City's director of Football Hugo Viana said: “We are all delighted that Pepijn and James have joined our senior coaching set-up.
“Pepijn and James have each amassed huge experience working in their individual roles over the past few years. Their talent, application, work ethic and all-round commitment are totally aligned with the values that underpin how Pep wants football to be played."
The pair replace Guardiola's former assistants Juanma Lillo, Inigo Dominguez and Carlos Vicens, who left Manchester City at the end of last season.
Pep, 42, originally joined Liverpool in 2014 under Brendan Rogers before staying on when Jurgen Klopp took over in 2015.
The Dutchman briefly left Merseyside to become head coach of Eredivisie side NEC in 2018 but was let go at the end of the season and returned to Liverpool.
He departed the Reds when Klopp left at the end of the 2023/24 season and became manager of Red Bull Salzburg - which is owned by Red Bull GmbH, for whom Klopp works as head of football - but left there last December.
Meanwhile French, who has experience with the Welsh FA, was an opposition analyst for Liverpool for over a decade after joining in 2012.