Young children with developmental disabilities (DDs) experience motor skill deficits compared to their peers without disabilities. Even though parents play an important role in developing their children’s motor skills, it has not been widely studied how parental behaviors influence motor skill development in young children with DDs. Therefore, the current study has two main purposes: (a) to examine early motor skill development of preschool aged children (3–5 years) with DDs longitudinally over a two-year period and (b) to longitudinally examine the relationship between parental behaviors and the motor skill development of young children with DDs. Fundamental motor skills (locomotor and object control skills) in 64 young children with DDs and their parent’s behavior was measured at five time points when children were between the ages of three and five years. Multilevel modeling was used to examine motor skill progression in young children with DDs and to evaluate the longitudinal relationship between parenting behaviors and motor skill development in young children with DDs. Findings indicated that young children with DDs develop their motor skills in a non-linear fashion across two years. Young children with DDs who have parents with one standard deviation higher (+ SD) in the positive parental behavior than average showed a statistically significant linear increase in the standard scores of locomotor and object-control skills with age (b = 0.27, p = 0.01; b = 0.22, p < 0.01, respectively). This study highlights the importance of positive parenting behaviors in regard to promoting motor skills in young children with DDs.