Several studies suggest that inhibition difficulties among people with ASD might be related to atypical cardiac vagal control. We examined how low versus high baseline heart rate variability (HRV) influences prepotent response inhibition in 31 males with autism spectrum disorder (ASD; mean age: 32.2; mean IQ: 107.8) compared to 39 typically developing (TD) males (mean age: 30.5; mean IQ: 102.0) by administering a stop signal task. Moreover, we examined whether adding an affective manipulation would alter findings and whether this manipulation affected HRV. Findings indicated that baseline HRV influenced inhibition in ASD males. Specifically, an ASD subgroup with low baseline HRV performed significantly worse compared to an ASD subgroup with high baseline HRV. No influence of baseline HRV was found in TD males. The affective manipulation did negatively influence performance and also altered HRV. Although replication is required, these first findings indicate that baseline cardiac vagal control seems to affect inhibitory control in males with ASD.