The Toffees secured the capture of midfielder Hornby, who is the younger brother of Cobblers midfielder Lewis, under the terms of the Elite Player Performance Plan (EPPP).
"We have mixed feelings as Fraser makes this move," said Cobblers academy manager Trevor Gould.
"We always want to keep our best players, but under the EPPP if a player is wanted by a Premier League club then it is just about impossible for us to resist given the processes set out as part of the EPPP.
"Fraser is going to a fantastic club with a proud record of producing young players who will continue his development."
The EPPP allows players to move to higher-ranked academies, with their original club receiving a fixed fee.