The purpose of the present study was to compare 3000 m running test results between 1969 and 2009 in a cohort of Norwegian high school pupils. Between 1969 and 2009, a total of 4981 (2827 boys) 3000 m running tests were collected from two Norwegian senior high schools. One-way ANOVA with Tukey's post hoc test was used to analyze the differences in the running times between the different decades. The running times have increased by 10% and 6% from the 1980s to the 2000s for boys and girls, respectively. The distribution showed a decline in aerobic fitness performance for all deciles. The largest negative change in difference was found for pupils with the poorest aerobic fitness level in both boys and girls. The cohort of 16- to 18-year-old boys and girls in the decade 2000–2009 had a poorer aerobic fitness performance in the 3000 m running test compared with earlier decades. The decline in running performance was greater for boys than girls, and the gap between the most and the least fit is becoming considerably larger.