•Salivary microRNAs (miRNAs) are promising biomarkers for identifying sports-related concussion.•This study investigated if concussion-related miRNAs are confounded by exercise.•Two miRNAs decreased with acute exercise and 23 changed over an athletic season.•Levels of miR-27a and miR-30a distinguished concussed and non-concussed athletes.•Saliva miRNAs may identify sports concussion without confounding effects of exercise.