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.
"I think the environment here will enable Seamus to develop his game and give him ample opportunities to impress."
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.