The club started life as Hoylake WFC in 1983. They merged with Dolphins YC to become Leasowe, then added Pacific to their title in a sponsorship deal. In 1987–88 they came to prominence winning the North West League and reaching the 1988 Women's FA Cup final, losing to Doncaster Belles 3–1. They were back the following year and this time they beat Friends of Fulham, this time on the right end of a 3–2 scoreline. By 1991–92 they had won their regional league five years running, and when the regular national competition was expanded the next season they were admitted to Division One North and promptly finished top to join the FA Women's Premier League.
In 1995 the club became known as Everton Ladies and continued to make their mark. In 1997 they reached the final of the Premier League Cup only to lose to Millwall Lionesses 1–2. The following year, however, Everton Ladies were crowned National Premier League Champions which is their biggest success to date.
In 1999 the club again lost in the League Cup final, 1–3 to Arsenal Ladies, and in 2005 reached the FA Women's Cup final only to lose 0–1 to Charlton Athletic after a disappointing display. Revenge of sorts came two years later when Everton pipped Charlton to second place in the Premier League, which as champions Arsenal had already won the UEFA Women's Cup, meant a European debut for the Toffees in 2007–08. In 2008 they won the Premier League Cup, by beating Arsenal in the final. Arsenal was unbeaten in England two years then.
The ladies' first foray into UEFA competition saw them win their opening game against local Lithuanian side Gintra 4–0. They won further group games against Glentoran and Zulwil without conceding and scoring 20 goals in the process. The campaign was to end in disappointment at the second group stage. Despite beating Valur 3–1 in their final group game, Everton only finished third and failed to progress into the quarter–finals amidst much controversy.
On 10 May 2009, Everton needed only a draw against Arsenal Ladies in the last match of the season to win the Women's Premier League for only the second time in their history, but lost 1–0 to finish runners–up on goal difference. Due to the reformatting of the European Cup into the UEFA Women's Champions League, however, they still qualified for Europe, although they had to enter at the qualifying group stages and were eliminated in the Round of 32 by Norway's Roa IL. In 2010 Everton beat Arsenal 3–2 to win the FA Women's Cup with Natasha Dowie (niece of Iain) scoring the winner deep into extra time.
In 2011 the club advanced to the quarter–finals of the Champions League; where their best run so far was stopped by German side FCR Duisburg. Everton were one of eight founding teams in the FA WSL in March 2011.
In 2014 after 21 years of top flight football they were relegated into the WSL 2.