The 24-year-old Mallon, whose appearances for the province have been limited this season following the arrival of international veteran Kevin Maggs, was originally recommended to Northampton by ex-Ulster boss Alan Solomons when he was in charge at Franklin's Gardens.
Derry-born Mallon, a member of the Ireland Sevens squad, has signed a two-year deal with the Saints, who also secured the services of Leinster centre David Quinlan in May.
Northampton head coach Budge Pountney said of his club's 11th new signing: "Seamus needed a change from Ulster and will relish the chance to prove himself here at Northampton.
Ulster supremo Mark McCall admitted: "Seamus' opportunity for game time with us has been limited, so the chance to be involved with a club like Northampton will provide him with excellent potential for his development."
Mallon made just three appearances for Ulster last season - all in the Celtic League.