Background Brain imaging has shown that not only the cortico-spinal tract (CST), but also alternate corticofugal motor fibers (aMF), such as the cortico-rubro-spinal and cortico-reticulo-spinal tract, influence residual motor output after stroke. So far, studies mainly have investigated each tract separately. A combined analysis of CST and aMF with assessment of their interactive role, i.e., that structural integrity of one tract influences the functional role of the structural integrity of the other, is pending. Methods 39 late subacute stroke patients (aged 59.4 ± 12.0 years, 100 ± 11 days after stroke) were included. Probabilistic tractography was used to reconstruct CST and aMF. Fractional anisotropy (FA) was calculated as a measure of microstructural integrity. Multiple-linear-regression analysis was used to associate tract-related FA with residual motor output and to determine interactions between CST and aMF. Results Both CST (coefficient = 3.93, p < 0.0001) and aMF (coefficient = − 4.43, p = 0.003) of the affected hemisphere significantly contributed to residual motor output. An interaction of their impacts with a consecutive influence on motor output was not detected (p = 0.882). Thus, these data suggest that aMF and CST explain residual motor output in stroke patients in a synergistic, but mainly independent manner. Conclusions The structural states of the CST and also – to a smaller degree – of the aMF correlate with residual motor output in late subacute stroke patients. Based on this statistical modeling with all inherent limitations, the novel finding of an absence of a significant interaction between both tracts in regard of their functional role, suggests that both corticofugal pathways act synergistically but largely independently. These findings add to the understanding of the functional role of different corticofugal motor fibers and their interactions for motor output after stroke.