The 19-year-old striker has signed what the Magpies described as a long-term deal and will initially work with Peter Beardsley's development squad.
Toney follows the respective arrivals at St James's Park of Georginio Wijnaldum, Chancel Mbemba and Aleksandar Mitrovic.
Newcastle said in a statement on their official website: "Newcastle United have completed the signing of striker Ivan Toney from Northampton Town.
"The 19-year-old moves to St. James' Park for an undisclosed fee and has signed a long-term deal with the Magpies."
Toney became the youngest player in Northampton's history when he made his debut for the club in 2012 at the age of just 16.
Beardsley added: "We have been very impressed with Ivan already.
"He is a very good player, with great enthusiasm and a first-class attitude, and has all the attributes to have a bright future at the Club."