Mallinder has signed a three-year contract and will be assisted at Franklin's Gardens by Dorian West.
The pair led the England Saxons to victory in the Barclays Churchill Cup at Twickenham last weekend.
Following Northampton's request, the Rugby Football Union have granted Mallinder and West early release from their positions at the national academy.
With Mallinder taking up his post immediately, acting head coach Peter Sloane will leave the club.
Northampton were in the market for a new director of rugby after Paul Grayson was moved to backs and skills coach following the Saints' relegation from the Guinness Premiership.