Background: Although fruits and vegetables are considered a pillar of healthy eating, previous evidence suggests that their consumption in Eastern European countries is low, and their association with health outcomes has rarely been researched in this region. Aim: To examine the effect of fruit and vegetable intake on self-rated health (SRH) in the Czech arm of the Health, Alcohol and Psychosocial factors in Eastern Europe prospective cohort study. Methods: Dietary data on fruit and vegetable intake was measured at baseline using food frequency questionnaires, and SRH from the second wave was chosen as the main outcome. The relationship between fruit and vegetable intake and SRH was analysed using multivariable ordinal regression. Results: A total of 4255 persons aged 45–69, in good and very good SRH at baseline were included in the longitudinal analysis, with a median follow-up time of 3.7 years. In the second wave, 218 (5.1%) individuals reported poor or very poor SRH. In the fully adjusted model, individuals in the lowest fruit and vegetable intake quartile had higher odds of poor SRH compared to those in the highest quartile (OR = 1.24, 95% CI: 1.01–1.52). When examined separately, the results were similar: for vegetables (OR = 1.25, 95% CI: 1.03–1.51) and fruit (OR = 1.18, 95% CI: 0.97–1.44). Conclusion: The observed longitudinal association suggests that low fruit and vegetable intake is associated with poor SRH in the Czech Republic. Considering almost half of our sample reported less than the daily recommended intake of 400 grams of fruits and vegetables, higher consumption should be supported.