The club was founded as Tayside Albion in 1887, changed their name to Newburgh West End in 1910, and assumed their current name in 1935.

The Scottish Junior Football Association (SJFA) restructured prior to the 2006–07 season, and Newburgh found themselves in the 12-team East Region, Central Division.

Newburgh have twice reached the semi-final stage of the Scottish Junior Cup, playing Renfrew in 1962 and Cambuslang Rangers in 1971.

Their quarter-final tie in 1962 against Irvine Meadow attracted a record crowd of 3,960 to East Shore Park.

In April 2020, Newburgh FC's application to join the East of Scotland Football League within the senior pyramid was approved at the association AGM.