A team representing Colwyn Bay played its first match in January 1881 and competed in the North Wales Coast Football League from 1901 until the competition folded in 1921 and the majority of clubs joined the Welsh National League.

The Bay won the League Cup in 1928 and were league runners-up in both 1928 and 1930, prior to the formation of the North Wales Football Combination, incorporating teams from Cheshire, and as founder members Colwyn Bay were league champions in the 1930-31 season. The club then joined the Birmingham & District League with the likes of Worcester City, Wrexham Reserves and Kidderminster Harriers, but found the travelling difficult and after finishing bottom for two season running, they resigned to join the Welsh League (North) in 1937.

The 1980s, however, that was the start of the most successful period for the club, winning the league title in 1983 and 1984. They also won the Cookson Cup in 1974, 1980, 1981, 1982, and 1984, the Barritt Cup in 1980 and 1984 as well as the North Wales Coast Challenge Cup in 1982, 1983, 1984, 1992 and 1996 and 1998. In 1984, the club crossed the border with election to the Bass North West Counties League and also moved from their old ground in Eirias Park to a new base in Llanedlian Road.

The club was promoted from the Third Division in their first season and following re-organisation of the leagues in 1987, the club was promoted to the First Division. Under manager Bryn Jones, they reached the Final of the Raab Karcher League Cup Final where they lost to Warrington Town at Gigg Lane, Bury, and reached the First Round Proper of the FA Cup for the first time in their history, losing 1-0 away to Northwich Victoria.

The following season they were in the Raab Karcher Final again and gained revenge over Warrington with a 3-0 win. In 1990-91 the club finished runners up to Knowsley United, but due to the demise of South Liverpool FC a vacancy was created in the Northern Premier League, and despite a strong challenge from North Shields, Colwyn Bay were elected.

In October 1991 news broke that the Football Association of Wales were to create a new League of Wales and would withdraw permission for non league clubs to play in England. The FA of Wales was challenged by the clubs, but the appeal was turned down. To the credit of the players and management, they went on to secure a league and cup double as well as the North Wales Coast Challenge Cup, and reached the semi-final of the Welsh Cup semi-final with a 3-1 win over a Wrexham side who only days earlier had beaten Arsenal in the FA Cup.

At the end of a highly successful first season in the NPL, the club had a big decision to make and gave it’s supporters a choice - either join the new League of Wales or go into exile whilst the club continued its battle with the Welsh FA alone through the courts for the right to play in the English pyramid. Financially, the club's choice to go into exile was not easy, but was supported by the local council, townspeople and supporters alike, and the fight was won in April 1995 when the High Court in London ruled the FAW demands constituted a restraint of trade.

At the end of the season 2000-2001 Bryn Jones stepped down as manager after 18 years at the helm to be replaced by long serving centre half Colin Caton, but in 2002-2003, the Bay were relegated for the first time in their history and Caton stepped down as manager, with the club struggling financially. A new group of directors took over part way through 2004, with a new clubhouse opened in Easter 2005, and the team under Gary Finley's managership reached the NPL play-offs before losing 3-2 in injury time to Cammell Laird.

Following a disappointing start to the 2008-09 season under Steve Pope, Neil Young was appointed as the new manager, assisted by former Tranmere Rovers and Nottingham Forest player Gary Jones and the team rose from 17th to 3rd place, securing two successive UniBond ‘club of the month’ awards for February and March along the way. The team eventually secured a play-off position, but were beaten away at Newcastle Blue Star on penalties in the semi-finals. The following season saw them in the play offs again and this time they went on to win promotion to the Premier Division, winning the final 1-0 at Lancaster City with a late Ian Sheridan penalty.

Manager Neil Young then left to join re-formed Chester, but club captain and ex-Tranmere Rovers defender Dave Challinor was installed as player/manager and with assistant Colin Woodthorpe guided the Bay to a second successive promotion. Rarely outside the play off places, they went on to beat FC United of Manchester 1-0 in the play-off final with Jon Newby's goal securing promotion to the Blue Square Conference North. Challinor and Woodthorpe, dropped a bombshell in October 2011 by leaving to take over at AFC Fylde and Newby took over as player-manager.

He won the league's Manager of the Month award within three months of taking over and successfully kept the team in the Conference North with a 12th place finish in their first season. The follow season, however, was a struggle on a tight budget and Newby was sacked in January 2013 after some disappointing results. Following a dismal month under Lee Williams, the club appointed ex-Chelsea and Leicester City defender Frank Sinclair as their new manager and he engineered a tremendous finish to the season as the team won six games in the space of 15 days to secure their Conference North status.

They finished a healthy 12th the following season, but after 23 months in the job Sinclair left by mutual agreement in January 2015 after a poor run of results and assistant Gus Williams was unable to save the team from being relegated on goal difference. A second successive relegation followed, with two managers, Ash Hoskin and then Kevin Lynch, unable to halt the slide.

Now back in the Evo-Stik League North, the club appointed Paul Moore as boss at the start of the 2016-17 season but he was sacked in December with assistant Phill Hadland taking over. The team finished the 2016-17 season in 15th place but remain ambitious and determined to climb back up the pyramid ladder.