Background Research has consistently indicated that most children do not consume sufficient fruit and vegetables to provide them with a healthy, balanced diet. This study set out to trial a simple, low-cost behavioural nudge intervention to encourage children to select and consume more fruit and vegetables with their lunchtime meal in a primary school cafeteria. Methods Four primary schools were randomly allocated to either the control or the intervention condition and baseline data were collected over two days in each school. Following this, changes were made to the choice architecture of the school cafeterias in the intervention schools and maintained over a three-week period. The intervention included improved positioning and serving of fruit, accompanied by attractive labelling of both fruit and vegetables on offer. Next, data were collected over two days in each school, with menus matched in each instance between baseline and follow-up. We employed a validated and sensitive photographic method to estimate individual children’s ( N = 176) consumption of vegetables, fruit, vitamin C, fibre, total sugars, and their overall calorie intake. Results Significant increases were recorded in the intervention schools for children’s consumption of fruit, vitamin C, and fibre. No significant changes were observed in the control condition. The increases in fruit consumption were recorded in a large proportion of individual children, irrespective of their baseline consumption levels. No changes in vegetable consumption were observed in either condition. Conclusions These results are the first to show that modest improvements to the choice architecture of school catering, and inclusion of behavioural nudges, can significantly increase fruit consumption, rather than just selection, in primary-age children. This has implications for the development of national and international strategies to promote healthy eating in schools. Trial registration AsPredicted: 3943 05/02/2017. URL: https://aspredicted.org/see_one.php?a_id=3943