The club was formed on Monday 4 June 1945 when a public meeting was held in the old wooden clubhouse at Brig O’Lea.

Renfrew District Council took over Brig O’Lea Stadium in the early 1960s and built a new clubhouse and installed floodlights for season 1964–65.

On 6 October 1998 Neilston won their first major trophy in 51 years by defeating Ballieston 5–0 at Fir Park, Motherwell in the Beatons Sectional League Cup Final.

Season 2002–03 saw Neilston come close to being crowned the first ever champions of the newly created West Super League Premier Division but they missed out on goal difference to Pollok.

[3] Neilston moved to the newly formed West of Scotland League in 2020 with members voting to drop the "Juniors" part of the club's name.