Purpose Our aim was to investigate lubricin, cartilage oligomeric matrix protein (COMP), and femoral cartilage deformation in response to different biomechanical loading of the knee joint (running vs cycling). Methods Serum lubricin and COMP concentrations (enzyme-linked immunosorbent assay), and femoral cartilage thickness (suprapatellar transverse ultrasonography) were determined in 11 male runners (age: 40 ± 6 years; weight: 76 ± 8 kg) and 11 male cyclists (35 ± 12 years; 75 ± 5 kg) at baseline, immediately after, and 30 min after vigorous exercise (time trial: 10-km run or 25-km cycle). Results At baseline, lubricin (runners: 104.0 ± 19.8 ng/ ml; cyclists: 119.1 ± 23.9 ng/ml) and COMP (runners: 804.1 ± 87.5 ng/ml; cyclists: 693.0 ± 84.7 ng/ml) did not significantly differ; however, vigorous exercise was accompanied by an increase in lubricin (cyclists: 39.4 %; p < 0.05; runners: 56.9 %; p < 0.05) and COMP (cyclists: 32.1 %; p < 0.05; runners: 14.2 %; p = 0.14) that returned toward baseline following 30 min of rest (p < 0.05). No between-group differences were observed for baseline cartilage thickness at the intercondyle notch, medial condyle, and lateral condyle, and vigorous exercise did not result in significant change for either group. Conclusions In the absence of ultrasonographic knee cartilage deformation, the response of serum lubricin and COMP following acute vigorous exercise indicates an increase in joint lubrication and cartilage metabolism, respectively, which appears largely independent of exercise modality.