It has been suggested that task-specific changes in neurophysiological function (neuroplasticity), should be assessed using testing modalities that replicate the characteristics of the intervention. The squat is a commonly prescribed resistance exercise that has been shown to elicit changes in central nervous system (CNS) function. However, previous studies have assessed squat-induced neuroplasticity using isometric knee extension, potentially confounding the results. The present study aimed to assess the agreement between corticospinal and intracortical activity relating to the knee extensors during isometric knee extension compared to an isometric squat task. Eleven males completed a neurophysiological assessment in an isometric squat (IS), and knee extension (KE) task matched for joint-angles (hip, knee, and ankle). Single- and paired-pulse transcranial magnetic stimulation (TMS) were delivered during isometric contractions at a range of intensities to assess short-interval cortical inhibition (SICI) and corticospinal excitability. Group mean values for SICI (70 ± 14% vs. 63 ± 12% of unconditioned MEP during IS and KE, respectively) and corticospinal excitability (mean differences 2-5% of Mmax at 25, 50, 75 and 100% MVC between the IS and KE) were not different between the two tasks (P > 0.05) in the vastus lateralis (VL). However, limits of agreement were wide, with poor-to-moderate average ICCs (SICI: ICC3,1 = 0.15, corticospinal excitability: average ICC3,1 range = 0.0-0.63), indicating disparate corticospinal and intracortical activity between the IS and KE. These data highlight the importance of task-specificity when assessing the modulation of corticospinal excitability and SICI in response to interventions resulting in neuroplastic changes.