Background Attention‐deficit/hyperactivity disorder (ADHD)‐like symptoms are common in fetal alcohol spectrum disorders (FASD). FASD and ADHD groups both display executive function impairments; however, there is ongoing debate whether the pattern and magnitude of executive function deficits differs between these two types of disorders. Methods An electronic literature search was conducted (PubMed, PsychInfo; 1972–2013) to identify studies comparing the executive functioning of children with FASD with ADHD or control groups. FASD groups included those with and without dysmorphy (i.e., FAS, pFAS, ARND, and other FASD diagnoses). Effect sizes (Hedges' g, standardized mean difference) were calculated. Random effects meta‐analytic models were performed using the metafor package for R. Results Fifty‐one studies met inclusion criteria (FASD N = 2,115; ADHD N = 453; controls N = 1,990). Children with FASD showed the strongest and most consistent deficits in planning, fluency, and set‐shifting compared to controls (Hedges' g = −0.94, −0.78) and children with ADHD (Hedges' g = −0.72, −0.32). FASD was associated with moderate to large impairments in working memory, compared to controls (Hedges' g = ‐.84, ‐.58) and small impairments relative to groups with ADHD (Hedges' g = ‐.26). Smaller and less consistent deficits were found on measures of inhibition and vigilance relative to controls (Hedges' g = −0.52, −0.31); FASD and ADHD were not differentiated on these measures. Moderator analyses indicated executive dysfunction was associated with older age, dysmorphy, and larger group differences in IQ. Sex and diagnostic system were not consistently related to effect size. Conclusions While FASD is associated with global executive impairments, executive function weaknesses are most consistent for measures of planning, fluency, and set‐shifting. Neuropsychological measures assessing these executive function domains may improve differential diagnosis and treatment of FASD.