Background: Norwegian children consume less fruit and vegetables (FV) than recommended. In order to increase the intake, a School Fruit subscription programme is now offered to all Norwegian elementary and junior high schools. This programme has limited effect due to low participation by schools and pupils. However, recent evaluations of the programme offered for free have reported good effects in increasing FV intake. The purpose of the present study is to evaluate the long term effects of the Norwegian School Fruit programme, provided at no-cost to the pupils, three years after it was provided for free. Methods: A total of 1950 (85%) 6th and 7th grade pupils from 38 Norwegian elementary schools participated in the project. Nine schools were selected as intervention schools and participated for free in the Norwegian School Fruit programme for a school year (October 2001 until June 2002). A baseline questionnaire survey was conducted in September 2001, and follow-up surveys were conducted in May 2002 and May 2005. FV intake was assessed by a written 24-h recall (reporting FV intake at school and FV intake all day), and by four food frequency questions (reporting usual FV intake). Data were analysed by a linear mixed model for repeated measures. Results: The pupils in the free fruit group increased their FV intake compared to pupils in the control group as a result of the intervention. Some of the effect was sustained three years later. The estimated long-term effects for FV all day were 0.38 and 0.44 portion/day for boys and girls, respectively. Conclusion: The results show long-term effects of a free school fruit programme.