Abstract Background Active school transport (AST) has declined rapidly in recent decades. While many studies have examined walking, cycling to school has received very little attention. Correlates of cycling are likely to differ to those from walking and cycling enables AST from further distances. This study examined individual, social and environmental factors associated with cycling to school among elementary school-aged children, stratified by gender. Methods Children (n = 1197) attending 25 Australian primary schools located in high or low walkable neighborhoods, completed a one-week travel diary and a parent/child questionnaire on travel habits and attitudes. Results Overall, 31.2% of boys and 14.6% of girls cycled ≥ 1 trip/week, however 59.4% of boys and 36.7% of girls reported cycling as their preferred school transport mode. In boys (but not girls), school neighborhood design was significantly associated with cycling: i.e., boys attending schools in neighborhoods with high connectivity and low traffic were 5.58 times more likely to cycle (95% CI 1.11-27.96) and for each kilometer boys lived from school the odds of cycling reduced by 0.70 (95% CI 0.63-0.99). Irrespective of gender, cycling to school was associated with parental confidence in their child's cycling ability (boys: OR 10.39; 95% CI 3.79-28.48; girls: OR 4.03; 95% CI 2.02-8.05), parental perceived convenience of driving (boys: OR 0.42; 95% CI 0.23-0.74; girls: OR 0.40; 95% CI 0.20-0.82); and child's preference to cycle (boys: OR 5.68; 95% CI 3.23-9.98; girls: OR 3.73; 95% CI 2.26-6.17). Conclusion School proximity, street network connectivity and traffic exposure in school neighborhoods was associated with boys (but not girls) cycling to school. Irrespective of gender, parents need to be confident in their child's cycling ability and must prioritize cycling over driving.