This study used a statistical parametric mapping method to compare temporal patterns knee joint loads and moments in cyclists pedalling using different saddle heights. Ten recreational cyclists pedalled using three saddle heights (Preferred, High and Low) during a single session. High and Low saddle heights were determined based on dynamically measured knee flexion angles (±10° from their Preferred height). 3D angles for the hip and knee and knee moments and forces were computed using a musculoskeletal model driven by 3D full-body motion and pedal forces. Knee flexion angles presented significant differences between saddle heights for the full crank cycle, without differences for hip adduction/abduction. Patellofemoral force was less for the Preferred compared to the High and Low saddle heights and for the High compared to the Low saddle heights between ~70-160° of the crank cycle. Right tibiofemoral anterior-posterior shear force was reduced for the Preferred compared to the Low saddle heights, without significant effects for the left tibiofemoral joint (p = 0.29-1.00). Large differences in temporal patterns for knee flexion due to changes in saddle height were followed by differences in patellofemoral force mostly when low force magnitudes were being transmitted between the femur and the patella.