The purpose of this study was to examine differences in sports participation and the levels of physical activity (PA) and sedentary behaviour (SB) between schoolchildren with cystic fibrosis (CF) and a healthy control group (CG) taking into account the gender variable. PA and SB were measured with an accelerometer for 7 consecutive days in 44 children (24 girls; 11.0 (3.2) years) with CF and 45 age-, sex-, and socioeconomic status-matched controls (24 girls; 11.1 (3.0) years). CF patients and CG did not differ in moderate-to-vigorous PA (54 (31) vs. 59 (27) min/day respectively) or in SB (558 (106) vs. 553 (92) min/day respectively). There were no differences in meeting the PA guidelines between both groups (CF: 36.4% vs. CG: 42.4%). Gender analysis revealed that boys were more active and met more PA guidelines than girls regardless of the group (CF or CG), girls with CF being the least active group (only 16.7% met PA guidelines). A possible compensatory effect was found between SB and PA only in the CF sample, as for each minute/day spent in SB the odds of meeting PA guidelines decreased by 34%. These findings suggest that promoting a reduction in SB is as important as promoting PA in the CF population, especially in girls. Health caregivers, coaches, teachers, or parents could offer appealing supervised and unsupervised physical activities, foster the adoption of active lifestyles, or incorporate PA into daily routines to improve the health of CF schoolchildren.