Background: Previous research suggests that children with or at risk of probable developmental coordination disorder (pDCD) activate different areas of the brain when performing certain motor skills compared with typically developing (TD) children. This study used functional near-infrared spectroscopy to compare prefrontal cortex (PFC) activity in TD and pDCD during the completion of manual (three-dimensional [3D]) and computerized versions (two-dimensional) of the Tower of Hanoi (ToH) puzzle. Method: A total of 12 children (TD and pDCD; one female/11 male, [x-bar] = 10.36, SD ± 1.52 years) performed the two-dimensional and 3D conditions of the ToH disk tasks, with equivalent executive function but different motor requirements, with functional near-infrared spectroscopy to compare PFC activity. Results: Interestingly, brain oxygenation levels were more apparent in the 3D versus two-dimensional ToH. In the 3D, there were large differences between pairs of discordant sibling sets and this was located to the right medial PFC, with pDCD exhibiting less activation in this region. Conclusion: While only exploratory, we have identified potential differences in the right medial PFC region, which differs within sibling sets with different pDCD status. These results concur with previous studies and are an area that needs to be explored further with a larger cohort of TD and pDCD.