Long-term day-to-day monitoring of physical activity (PA) has not been undertaken in adolescents despite PA declines rapidly during adolescence. This study monitored the school year-round pedometer-determined PA of pupils attending high school in the Czech Republic. We assessed their PA levels; appraised the school year-round variability of their PA; and, assessed the associations between their PA levels and weekdays/weekends; months; seasons; and physical education (PE) lessons at school. We observed the PA levels of 10 girls and 2 boys (aged 16.0 ± 0.7 years). Each pupil wore an unsealed pedometer (Omron HJ-105) on the right side of the waist continuously for one year, and recorded steps/day and daily behaviour (e.g. after-school PA, PE lesson) into an activity diary. In total, participants recorded step counts for 2,979 person- days (82.0% of a possible 3,628 person-days). We used the Missing Values Analysis EM function of SPSS to estimate step values that were missing from the dataset. The sample’s mean daily step count was 14,727 ± 6,612 steps/day, and repeated ANOVA showed differences in steps/day across the days of the week (p < 0.0001), months (p < 0.0001) and seasons (p < 0.0001). The mean number of steps/day for weekdays (15,733 ± 6,354) was higher (p < 0.0001) than weekends values (12,196 ± 6,574), and was higher for days with PE lesson (17,280 ± 5,988) than for days without PE lesson (15,569 ± 6,318) (p < 0.0001). The total contribution of PE class (90 minutes) to pupils’ daily PA was 10.0% additional steps per PE day. In conclusion, this study contributes to understanding the day-to-day PA variability of adolescent pupils across the school year. Across all months and seasons, pupils achieved notably more steps on weekdays than on weekends; and on PE days than on non-PE days. Research is required to assess these findings for school pupils in other countries.