Anterior knee pain (AKP) is a frequent clinical presentation in jumping athletes and may be aggravated by sustained sitting, stair use, and loading of the quadriceps. Corticospinal activation of the quadriceps in athletes with AKP has not yet been investigated, but is important in guiding efficacious treatment. This cross-sectional study assessed corticospinal excitability (CSE) of the quadriceps in jumping athletes using transcranial magnetic stimulation (TMS). Groups consisted of Control (no knee pain); patellar tendinopathy (PT) [localized inferior pole pain on single-leg decline squat (SLDS)]; and other AKP (nonlocalized pain around the patella). SLDS (numerical score of pain 0-10), Victorian Institute of Sport Assessment Patellar tendon (VISA-P), maximal voluntary isometric contraction (MVIC), active motor threshold (AMT), CSE, and Mmax were tested. Twenty nine athletes participated; control n = 8, PT n = 11, AKP n = 10. There were no group differences in age (P = 0.23), body mass index (P = 0.16), MVIC (P = 0.38) or weekly activity (P = 0.22). PT had elevated CSE compared with controls and other AKP (P < 0.001), but no differences were detected between AKP and controls (P = 0.47). CSE appears to be greater in PT than controls and other AKP. An improved understanding of the corticospinal responses in different sources of knee pain may direct better treatment approaches.