A prospective, non-randomized comparative study was conducted to compare the distribution of oculomotor and visual alterations in children with neurodevelopmental disorders and healthy children without such disorders. Sixty-nine children (aged 6–13 years) were enrolled and divided into three groups: a control group (CG) of 23 healthy children; a group of 18 healthy children with oculomotor abnormalities (OAG); and a group of 28 children with a neurodevelopmental disorder (NDDG), with 15 cases of dyslexia, 7 cases of developmental coordination disorder (DCD) and 6 cases of attention deficit/hyperactivity disorder (ADHD). Significantly worse near stereopsis was found in NDDG compared with CG (p < 0.001) and OAG (p = 0.001). Likewise, a significantly lower amplitude of accommodation was found in NDDG compared with CG in both the right (p = 0.001) and left eyes (p < 0.001). No statistically significant differences between groups were found in the measurement of near and distance phoria (p ≥ 0.557), near point of convergence (p = 0.700) and fusional vergences (p ≥ 0.059). Significantly impaired oculomotor test scores were found in NDDG compared with CG (p < 0.001), with no significant differences between OAG and NDDG (p ≥ 0.063). The comparison between the three types of neurodevelopmental disorders included revealed the presence of a significantly lower amplitude of accommodation in children with DCD compared with dyslexics. Furthermore, less exophoria at near was present in children with dyslexia compared with children with ADHD (p = 0.018) and DCD (p = 0.054). In conclusion, children with dyslexia, ADHD and DCD show an altered oculomotor pattern and a more reduced amplitude of accommodation, not always compatible with the diagnostic criteria of an accommodative insufficiency. Accommodative and binocular vision problems are not always present in these children and cannot be considered an etiologic factor.