Muscle fat infiltration (MFI) is an expected consequence of incomplete spinal cord injury (iSCI). The MFI magnitude may have clinical value in determining functional recovery. However, there is a lack of understanding of how MFI relates to the volitional muscle activity in people with motor incomplete spinal cord injury (iSCI). Five iSCI and 5 uninjured age-matched control subjects participated in the study. In this preliminary study, we established the reliability of MFI quantification of select lower extremity muscles across different raters. Secondly, we assessed the magnitude and distribution of MFI in the lower legs of iSCI and uninjured control participants. Thirdly, we explored the relationship between MFI in the plantar flexor muscles and the ability to volitionally activate these muscles. High levels of inter-rater reliability were observed. The iSCI group had significantly elevated and a vastly different MFI distribution in the lower leg muscles compared to healthy controls. MFI was negatively correlated with volitional activation in iSCI. Our preliminary results sanction the importance of lower extremity MFI quantification as a potential measure in determining the functional outcomes in iSCI, and the subsequent pathological sequelae.