The profile of executive function (EF) in adults with Schizophrenia (SCZ) and autism spectrum disorder (ASD) remains unclear. This study aims to ascertain if distinct EF patterns can be identified between each clinical condition by comparing the neuropsychological profile of adults with SCZ and ASD, for whom the differential diagnosis is still highly challenging. Forty-five individuals (15 SCZ, 15 ASD, 15 controls) matched for age, sex, education level, and handedness underwent intelligence evaluation and neuropsychological testing for working memory, inhibition, planning and set-shifting, and verbal fluency subdomains. Principal component analysis (2D-PCA) using variables representing 4 domains was employed to identify patterns in neuropsychological profiles. The ASD group had lower scores on the Digits Forward subtest compared to the SCZ group (7.2 ± 2.1 vs. 9.3 ± 1.9, p = 0.003; Cohen’s d: 1.05). ASD also performed significantly worse on the Stroop Word Test compared to the control group (77.7± 17.9 vs. 98.0 ± 12.7, p = 0.009; Cohen’s d: 1.31). No significant differences were observed between ASD and SCZ on other EF measures. The larger contributors for the dimensions in 2D-PCA were the Digits Forward subtest and Stroop Word Test. Still, there was substantial overlap between the clinical groups. This study suggests a high degree of similarity of EF between SCZ and ASD. Through four EF measures, the discrimination of low and high-functioning EF groups spanning both diagnostic categories may help to identify the individuals who could better benefit from cognitive rehabilitation strategies.