The Strengths and Difficulties Questionnaire (SDQ) is one of the most widely used measures of young people’s mental health difficulties in research and clinical decision-making. Although the SDQ is available in both paper and computer survey formats, cross-format equivalences have yet to be established. The current study aimed to assess the measure’s equivalence across paper- and computer-based survey formats in a community-based school setting. The study examined self-reported measures completed by a matched sample of 11–14 year olds in secondary schools in England (589 completed paper version; 589 online version). Analyses demonstrate that the factor structure, although did not vary by survey format, resulted in poorly fitting models limiting the use of model based invariance testing. Results indicate that the measure does not operate similarly across different formats, with scale-level mean differences observed for the hyperactivity scale, which also affects the total difficulties score, with higher scores seen in the paper version. Responses to the impact supplement were also influenced by survey format, with higher impact in specific domains disclosed on the computer-based measure. Item-level differential item functioning was observed for four items in the measure; two from the prosocial scale where the DIF is large enough to affect the scale (DTF, ν2 = 0.14). The inconsistency across survey formats highlights the need for more assessment of influences of different survey formats on young people, their perceived privacy and their mental health disclosures via different media. The findings also highlight the potential confounding effect of format when different methods of data collection are used, with a potentially substantive impact on cross-sample comparisons and within child clinical review.