The club was formed in 1955 by founding members Thomas Waugh (known locally as the unofficial mayor of Millisle) and Lennie Bennett along with his brothers Nelson, Tom, Raymond and Norman.

In 1962, Thomas Waugh followed the advice of fellow club chairman Herbie Johnstone and applied to join the Northern Amateur Football League.

The club had just moved into their new grounds at Adams Park (named after then manager Brian Adams) and on its debut season saw the club win Division 1B by 11 points and lift the Border Regiment Cup after a 5–0 win in the final over Drumaness Mills.

The club also had a successful Irish Cup run under Adams in 1995–96 reaching the last 16 before being knocked out by Lisburn Distillery.

Villa reached the Irish Cup 2007–08 they were knocked out of the sixth round after a narrow 1–0 defeat to Donegal Celtic.