You don't have to run for exactly 3 miles to burn calories. Shorter and longer runs also contribute to your overall calorie burn. The calories you'll burn over the course of your 3-mile run depend on your weight and pace.If a 125-pound person runs at a pace of 6 mph, she'll reach her 3-mile goal in 30 minutes.During this half hour of running, she'll burn about 300 calories. As your weight increases, so too does your rate of burning calories.f a 125-pound person runs at a pace of 6 mph, she'll reach her 3-mile goal in 30 minutes. During this half hour of running, she'll burn about 300 calories. As your weight increases, so too does your rate of burning calories.