Physical activity (PA) programs have been found to result in improved sleep in males with autism spectrum disorder (ASD), but little is known about the female characteristics. The aim of this work was to assess sex differences in sleep and PA indices using an accelerometer over 7 days and 7 nights. Sleep and PA variables were measured with questionnaires and with accelerometry in twenty-four children with ASD (16 boys, 10.3 ± 2.8; 8 girls, 11.1 ± 3.9). Some significant differences were reported between girls and boys. The total time in bed and wake time after sleep onset (WASO) were significantly higher in girls compared to boys (p < 0.01), whereas sleep efficiency was significantly lower in girls (p < 0.01). The results obtained from the sleep questionnaire (CSHQ) show averages above the threshold of 41 in both groups (the threshold indicates the presence of sleep disorders or low sleep quality). The number of daily steps was significantly lower in the girls' group (p < 0.01), and the PA volume for vigorous and strong vigorous intensities was significantly higher in the boys' group (p < 0.01 and p < 0.05, respectively). Our results show major alterations in girls, with a low level of PA and sleep alteration. PA is a relevant non-pharmacological approach to improve sleep quality and achieve sufficient sleep duration. However, particularly for girls with ASD, more personalized approaches to improve sleep may be needed to manage specific associated disorders.