The 53-year-old had been working with the Rugby Football Union on youth development, but has now accepted a role north of the border.
The SRU announced the news in a social media post on Friday morning.
Mallinder joined the England set-up in the summer of 2018 after spells in charge of Sale and Northampton.
He spent over a decade with the Saints, leading them back to the Premiership in 2008 and securing the European Challenge Cup the following year.
In 2014 the club won a Premiership and Challenge Cup double and Mallinder signed a new five-year deal with the midlands club, but was sacked in December 2017 after a poor run of results.
He had been considered as a candidate to step up to the position of England head coach. Current incumbent Eddie Jones is due to stand down in 2021, with the RFU keen to appoint a successor who can work alongside Jones initially in 2020.
Mallinder replaces Scott Johnson, who left the SRU in April, and will oversee the pathway from the feeder system into Scotland’s two professional teams, the national men’s and women’s 15-a-side and sevens teams.
Mallinder told the SRU’s official website: “This is an exciting role and one that gives me the chance to work with players at different stages of their development, all with the clear objective to make Scotland’s representative teams more successful and deliver a clear pathway for players to progress through.
“I am really impressed with the set-up in Scotland already and having spoken at length with (SRU chief executive) Mark Dodson it was clear that this was an outstanding opportunity to really set the direction of travel for Scotland’s high-performance ambitions.
“It’s a chance to lead a long-term programme, work with talented people, and I’m looking forward to moving up to Scotland and getting started.”