The scapula is a rare location for osteoid osteoma, which in most cases does not involve the flat bones. The en bloc excision in this uncommon location can be problematic since the surgical exposure is difficult, and shoulder joint function can be affected if the lesion is subchondral. In an 18-year-old man, an osteoid osteoma was located in the subchondral area of the glenoid. A guided needle biopsy of the nidus resulted in complete healing. This mode of treatment, with proper follow-up examination, is acceptable for a benign lesion situated in a problematic location.