Eynesbury Rovers were formed in 1897 and played village football in their early years. They won the Huntingdonshire Senior Cup for the first time in 1914 and won the county Junior Cup in 1921, 1927 and 1932. Competing in the Bedford & District League Eynesbury won 2nd Division championships in 1927, 1931 and 1932 and in 1934 they joined the South Midlands League.

Promotion was achieved at the first attempt while the Scott-Gatty Cup was won, while Senior Cup finals in 1937 and 1939 ended in defeat.

The post war era began with Rovers joining the UCL and they enjoyed spectacular cup success winning the Hunts Senior Cup and Hinchingbrooke Cup four times each in a five year period. Particularly memorable was the 1950-51 campaign when a Premier Cup success made it a cup hat trick.

In 1952 Eynesbury joined the Eastern Counties League finishing fourth in their second season. In 1955 a crowd of 5,000 packed into Hall Road to watch a friendly against Fulham with the legendary Stanley Matthews guesting for Rovers.

The club continued to enjoy cup success lifting the Senior Cup in 1955 and 1957, the Hinchingbrooke Cup in 1958 and Cambs Invitation Cup in 1962, but they were finding life difficult in the league. In 1963, after finishing bottom of the ECL for the second time in three years they rejoined the UCL.

Successes in the Hinchingbrooke Cup in 1967 and Hunts Senior Cup in 1970 masked a continued decline and relegation was suffered in 1972. Current chairman Brian Abraham's appointment as manager generated an upturn in fortunes and a top flight place was regained in 1977.

Floodlights were installed in 1981 with Luton Town providing the opposition for the official opening in front of a four figure crowd. The Hunts Senior Cup was won in 1985 and from 1988 to 1990 Rovers were beaten finalists three years running.

Gary Pilsworth enjoyed great success as manager, leading Eynesbury to a best ever third place in the league, two Hunts Senior Cup wins, a Premier Cup success and two East Anglian Cup finals, and Alan Day kept the momentum going with a 1993 Senior Cup success.

Barry Cavilla was next in the hot seat and he led Rovers to a best ever FA Vase run before the 1995-96 campaign saw Eynesbury finish fifth in the league and win both the Senior and Premier Cups.
The club's centenary in 1997 saw Sir Stanley Matthews, Graham Kelly and Wilf McGuinness attend the celebration dinner.
A success in the Hunts Senior Cup in 2000 was followed by relegation a year later. In 2002 Rovers again won the Senior Cup beating St Neots 3-0 in the final, while the 2003-04 campaign saw them reach the Premier Cup final only to lose 4-2 to Wootton, while a late slump in results saw Eynesbury finish fifth in the division after looking set for promotion earlier in the season.
In the summer of 2005 Dean Shipp was promoted to the position of first team manager, having previously lead the reserves to promotion in 2004. In his first season in charge Rovers finished in a credible 7th place in the league. Season 2006-07 was not so good though and a slump in league form saw them finish in 10th place. However, the season was not all bad, as Rovers went on to reach the final of the South Midlands Cup Final before, where they lost 2-1 to Saffron Walden.
In December 2007, following a poor half of the season, Dean Shipp resigned and Rovers appointed the management duo of Al Lenihan and former player Pat O'Keefe. The club finished the 2007/08 season in 13th place but are optimistic of challenging for promotion next season.