You can run in Cusco, but it takes commitment, thick skin, and a couple days of acclimatizing.
Of the few runners I saw, most looked as though they were sticking within a two-block radius of the Plaza de Armas. A young woman we met at a yummy crepe restaurant in San Blas (Creperia La Boheme) said she was paying a couple soles to use the track at the university. This may a good option if you're reasonably close to the university.
I tried a few routes during our month in the city (June-July 2014). This one gave me the best views and the fewest hassles.
|About 4.5 miles|
Start your run here. Head out to the main road, take a left, and make a circuit around Saksaywaman.
If you stay left after the Saksaywaman parking lot, you'll eventually find yourself on Don Bosco, sprinting downhill after a grueling half-mile (or so) uphill. The run ends in the Plaza de Armas.