Abstract Background: Physical activity is an important part of healthy lifestyle especially for autistic children. A few studies have previously compared the differences of diet intake and physical activity patterns in autistic and healthy children. This study was aimed to compare the macro-and micronutrient intake and physical activity patterns between children with and without autism. Materials and Methods: The present case-control study was conducted on 59 boys aged 6 to 13 years with autism and healthy children. Dietary intake of subjects was measured by Food Frequency Questionnaire (FFQ). The physical activity level was recorded for seven days using an ActiGraph accelerometer which categorized by the time of each participant spent, in sedentary, moderate and vigorous activity. Results: The findings revealed that there were significant differences in intake of many dietary factors including energy (p <0.05), carbohydrate (p<0.05), sugar (p<0.05), fructose (p<0.01), vitamin D (p<0.05), Vitamin C (p<0.01), Calcium (p<0.01), Iron (p<0.05), Magnesium (p<0.05) and Manganese (p<0.05) between autistic and healthy children. Furthermore, sedentary and moderate activity levels were significantly higher in children with autism compared with healthy children (p <0.05). Percent calories from fat was positively associated with heavy physical activity (r= 0.258, p<0.05). multivariate linear regression analysis showed that after control for change in BMI and dietary energy intake the calorie from fat, vitamin C and caffeine were negatively associated with physical activity level (r = -0.571, p <0.05 Vs. r= -0.573, p<0.05 Vs. r= -0.371, p<0.01, respectively). Conclusion: It is concluded that there is a significant difference in food intake and physical activity levels in children with autism compared with healthy children. The potential role of diet especially calorie from fat, vitamin C, and caffeine should be considered to have applicable physical activity recommendations for children with ASD.