Aims: There are well-known gender differences in smoking, including the pattern of use and the effectiveness of smoking prevention programs. However, little is known about the differences between boys and girls in their attitudes towards smoking prevention interventions. This study explores gender differences in attitudes towards a school-based intervention to prevent smoking. Methods: We used data from the X:IT II intervention study conducted in 46 Danish elementary schools. Results: Compared to boys, girls were more positive towards smoke-free school time, both concerning rules for teachers smoking (odds ratio (OR) = 1.69, 95% confidence interval (CI): 1.35–2.12) and for students smoking (OR = 1.41, 95% CI: 1.13–1.76). No difference was observed in students signing the smoke-free agreement. However, a larger proportion of girls reported that the agreement was a good occasion to talk about smoking with their parents (OR = 1.36, 95% CI: 1.13–1.76). Girls were also more positive towards the smoke-free curriculum (OR = 1.52, 95% CI: 1.19–1.94). Conclusions: This study showed that girls were, overall, more positive towards the components of the smoking preventive intervention. Our findings highlight the importance of considering differences in intervention preferences for boys and girls in future health prevention initiatives.