There is no official record of when or by whom the club was founded in Newlyn but a photograph exists of a young team in their football kit dated 1906. It could be that the club was formed around the same time as the Cricket Club by Canon Bone to provide a less exclusive sport than cricket and it subsequently became affiliated with the CCFA as a Junior Club in 1913.

It is recorded in CCFA history that, in the 1923/4 season, they were runners up to Torpoint Reserves in the Cornwall Junior Cup Final losing 4-1 and, in 1926 came third in the Cornwall Junior Cup (Western Division).

The 1960's proved to be a very successful decade for the club playing by now in the Cornwall Mining League. The club won a total of 6 cups over the ten years that included the Moon Shield and Whitford Cup in 1964, the Whitford Cup again in 1965 and in 1968 an unprecedented quadruple of Moon Shield, Whitford Cup, Dunn Cup and Hart Cup.

1970 saw the club enter the Duchy Football League for the first time and win the Division 2 title that year. The following season saw the team finish runners up to St Dennis Utd in the League Cup.

From the mid-nineties the club had 2 teams playing in the Duchy Football League. As well as a 1st Team the Reserve Team played in Division 4 allowing younger players to gain valuable experience before making the step up to a higher standard of football.

In the 1997/8 season the club completed a remarkable feat of winning 26 out of 26 league matches - a fantastic achievement at any level of football. The "invincibles" as they became known also secured the Division 2 Cup in the same season. In 2002/3 the club then won the Division 1 title and promotion to the Premier League, the Reserves continued to play in Division 4 of the Duchy Football League.

In 2007/8 the club was accepted to play senior football in the East Cornwall League. This was the first time our club had competed at this standard and marked the start of a new era of football at St. Newlyn East AFC. At the end of that season we retained our senior status and our Duchy League Team secured promotion to Division 3 marking a successful season for our club. Unfortunately the Club could not sustain a Senior side in the 2008/9 season and decided to move forward as a Junior Football Club once more. This saw the club gain 4 successive promotions including in 2010 winning the Duchy League Division 2 League title and finishing Runners-up in 2011.

The 2017/18 season saw The Saints win the Division 1 League title and gain promotion again to the Duchy Premier Division.

Its second season back in the Duchy Premier Division saw the club in contention to become champions and also in the semi-final of the CCFA Junior Cup before the COVID-19 Pandemic saw the season declared null and void. However the season brought an opportunity to re-join the East Cornwall Premier League and the club was elected to the higher level of local football for only the second time in its history.