The present study investigated the applicability of magnetic stimulation (MS) for estimating activation capacity. Ten men performed isometric knee extensions at 95% of maximum voluntary contraction level on two testing sessions. MS and electrical stimulation (ES) were applied by placing the coil and stimulating electrodes, respectively, on the quadriceps muscle group. In session 1, MS and ES were applied to allow a comparison between the two stimulating devices. During session 2, MS was applied again to assess the reproducibility of MS measurements. Activation level was estimated with the interpolated twitch technique (ITT) and the central activation ratio (CAR). Activation level determined with MS was highly repeatable, but was only comparable to ES when using ITT (standard error < 1.45%, mean difference < 0.63%, for all). MS with CAR overestimated activation by 3% compared to ES (standard error = 1.13%, mean difference = 2.76%) because the power of the magnetic field was limited. These results indicate that MS is a promising tool for reliable and valid quantification of activation levels when using the ITT approach and potentially suitable for studies involving children or other subjects where the pain of conventional ES is a problem.