I do morning jog two to three times a week. Jogging in Prague can be more than just exercise.
Prague is such a beautiful city, and in the day there are too many tourists, which makes it difficult to enjoy the city view. However, in the early morning around 7am, there are very little people at places like Charles Bridge, Old Town and other interesting area in the city. Thus I recommend jogging around the city in the morning while enjoying beautiful historical architectures without the crowd in Prague.
Moreover, we can always end the jogging sessions by warming down around nature with nice fresh air at a nearby park.