Sacral schwannoma is a rare tumor with relatively few symptoms; it thus tends to be large at diagnosis and is challenging to treat surgically. We present the case of a 12-year-old girl with a large sacral schwannoma that was successfully surgically resected using O-arm navigation in a two-stage operation. First, we performed tumor resection from the posterior aspect with assisted O-arm navigation. One week later, resection from the anterior aspect was conducted with posterior spinopelvic fixation and fibula graft. We performed partial resection of the tumor from the anterior and posterior aspects as much as possible. O-arm navigation contributed to precise and safe tumor resection and implant insertion.