The centre-back signed for the Blues on loan from the Toffees back in January, helping the club retain their WSL2 status with goals in wins against both Sheffield United and Sunderland.
She now departs Everton after four years on Merseyside, having previously spent time on loan at then WSL2 side Lewes and Scottish Women’s Premier League team Glasgow City.
"I'm really happy to have returned on a permanent basis having enjoyed my time here last season," Weir said after signing.
"There's a real ambition to now push on and I'm looking forward to being a part of making that happen."
Sean Burt, Town Women’s Technical Director, added: "It was a no-brainer to bring Kenzie back after the impact she made during the second half of last season, and we’re delighted that she was just as keen to return.
"Her presence in both penalty boxes played a huge part in our revival towards the end of the campaign, while her experience of being at a WSL1 club also helped drive standards off the pitch and had a real positive influence around the group. It’s fantastic she’s joined us on a permanent basis."
22-year-old Weir, who earned her first senior Scotland call-up back in April, is the daughter of former Everton defender David Weir.
TRACTOR GIRLS SIGNINGS SO FAR
Midfielder Jenna Slattery from Hearts
Midfielder Aimee Palmer from Southampton
Winger Rosie Livingstone from Hibernian
Winger Megan Hornby from Portsmouth
Forward Kit Graham from Spurs
Centre-back Georgia Hunter from Hearts
Forward Eilidh Adams from Hibernian
Striker Georgia Timms from Hearts
Winger Ava Baker from Birmingham City