The aim of the Finnish Schools on the Move program is to create a more active and pleasant school day through physical activity (PA). In this quasi-experimental design, we compared changes in moderate-to-vigorous-intensity physical activity (MVPA) and sedentary time (ST) during the school day and outside school hours for Grades 1–9 over two academic years in four program schools and two reference schools. Altogether 319 girls and boys aged 7–15 participated in the study between 2010 and 2012. MVPA and ST were measured four times over the 1.5-year follow-up period for seven consecutive days, using a hip-worn ActiGraph accelerometer. Linear growth curve modeling was used to examine the effect of the program on MVPA and ST during follow-up. School day MVPA increased (P = 0.010) and school day ST decreased (P = 0.008) in program primary schools (Grades 1–6) more compared with the reference schools. The effect sizes (Cohen's d) for the difference in change (from the first to the last measurement) were small (d = 0.18 and d = −0.27, respectively). No differences in the changes of leisure-time or whole-day MVPA and ST between the program and reference schools were observed during follow-up. In conclusion, the changes in school day MVPA and ST did not translate into positive effects across the whole day. More effective and longer promotion actions are needed for positive changes in PA and ST, especially in lower secondary schools and for all daily segments.