Objective To describe an ultrasound assisted arthroscopic approach for removal of non-articular basilar sesamoid fragments in Thoroughbred yearlings. Animals Thoroughbred yearlings (n = 7). Methods Basilar sesamoid fragments identified during pre-sale radiographic examination were removed using a palmar/plantar arthroscopic approach to the fetlock joint and ultrasonographic guidance. Complete fragment removal was confirmed by ultrasonography and radiography. Results Basilar sesamoid fracture fragments were localized and removed successfully using rongeurs and a radiofrequency probe for soft tissue dissection of the fragment. Complete fragment removal was confirmed by ultrasonography and radiography. No intra- or postoperative complications occurred. At 6–8 months follow-up, no fragments or bony proliferation at the base of the sesamoid was observed. Conclusions Ultrasonographic guidance can be used to facilitate localization, dissection, and confirmation of removal of basilar fragments of the proximal sesamoid bone.