The event organisers said the attraction had "showcased an incredible vision and dedication", with Railworld describing itself as having "crazy, passionate volunteers".
Peterborough attraction Railworld scoops prestigious award
John Devine/BBC
The awards ceremony was held at the Hilton Hotel in London last week.
Railworld won the joint top category prize for its "Entertain and Educate about our Amazing Planet" project, along with Stourbridge's Glass Museum for its eco-friendly upcycled glass exhibition.
Brian Pearce, 76, the chairman of Railworld, said: "When we saw that the Natural History Museum were in it [our category], we thought we'd have no chance."
John Devine/BBC
Attractions manager Becky White, 45, said it was wonderful to see the volunteers getting rewarded for their efforts, with the site celebrating its 40th anniversary.
"We have about 20 volunteers from all walks of life and they give so much, and hopefully make such a difference to the people of Peterborough and beyond," she said.
The award was supported by the National Lottery Heritage Fund and she hoped in future it could help provide a financial boost, as it looks to rebuild a Victorian railway station building at the site.