Bone stress injury (BSI) is a common overuse injury that can result in prolonged time away from sport. Limited studies have characterized the use of extracorporeal shockwave therapy (ESWT) for the treatment of BSI. The purpose of this study was to describe the use of ESWT for the management of BSI in runners. A retrospective chart review was performed to identify eligible patients in a single physician's clinic from 1 August 2018 to 30 September 2022. BSI was identified in 40 runners with 41 injuries (28 females; average age and standard deviation: 30 ± 13 years; average pre-injury training 72 ± 40 km per week). Overall, 63% ( = 26) met the criteria for moderate- or high-risk Female or Male Athlete Triad categories. Runners started ESWT at a median of 36 days (IQR 11 to 95 days; range 3 days to 8 years) from BSI diagnosis. On average, each received 5 ± 2 total focused ESWT treatments. Those with acute BSI (ESWT started <3 months from BSI diagnosis) had an average return to run at 12.0 ± 7.5 weeks, while patients with delayed union (>3 months, = 3) or non-union (>6 months, = 9) had longer time for return to running (19.8 ± 14.8 weeks, = 0.032). All runners returned to pain-free running after ESWT except one runner with non-union of grade 4 navicular BSI who opted for surgery. No complications were observed with ESWT. These findings suggest that focused ESWT may be a safe treatment for the management of BSI in runners.