Given the developmental inter-relationship between motor ability and spatial skills, we investigated the impact of physical disability (PD) on spatial cognition. Fifty-three children with special educational needs including PD were divided into those who were wheelchair users (n = 34) and those with independent locomotion ability (n = 19). This division additionally enabled us to determine the impact of limited independent physical exploration (i.e., required wheelchair use) on spatial competence. We compared the spatial performance of children in these two PD groups to that of typically developing (TD) children who spanned the range of non-verbal ability of the PD groups. Participants completed three spatial tasks; a mental rotation task, a spatial programming task and a desktop virtual reality (VR) navigation task. Levels of impairment of the PD groups were broadly commensurate with their overall level of non-verbal ability. The exception to this was the performance of the PD wheelchair group on the mental rotation task, which was below that expected for their level of non-verbal ability. Group differences in approach to the spatial programming task were evident in that both PD groups showed a different error pattern from the TD group. These findings suggested that for children with both learning difficulties and PD, the unique developmental impact on spatial ability of having physical disabilities, over and above the impact of any learning difficulties, is minimal.