Background: The microfracture (MF) technique is an established surgical treatment for cartilage injury. However, the early-phase histological changes in full-thickness cartilage defects (FTCDs) after MF and the concomitant changes in the subchondral bone are still unknown. Purpose: To determine the early-phase histological changes in FTCD associated with subchondral bone remodeling after MF in rat model. Study Design: Controlled laboratory study. Methods: Rats were subjected to FTCD, followed by MF at the trochlear groove. For histological analysis, experiment and untreated control rats were sacrificed at 0, 1, 3, 7, 14, 28, and 56 days postoperatively (n = 6 knees per time point). Cartilage healing response was evaluated with the Pineda score. Osteoclast activity was evaluated by counting and locating the number of tartrate-resistant acid phosphatase (TRAP)–positive cells in the subchondral bone. MF hole diameter and bone mineral density in the subchondral bone were measured sequentially in 3 rats (n = 6 knees) by 3-dimensional μ–computed tomography. Results: Pineda score showed no difference in cartilage response from day 0 to day 3 but a significant improvement from day 7 to day 56. Although the MF holes were filled with blood clots in all specimens, the defect sites were not. The number of TRAP-positive cells peaked at day 3, mostly accumulating around the deeper zone of the MF holes. Over time, the number of TRAP-positive cells decreased to preoperative levels, localizing around the aperture of the MF holes where there was active remodeling of the osteochondral unit. The MF hole diameter was largest at day 14, and most holes disappeared by day 28. Bone mineral density was also highest at day 14 and decreased to preoperative levels by day 56. Conclusion: Histological changes in the FTCD after MF were derived from endochondral ossification within the deeper zone of the MF holes. Clinical Relevance: The absence of healing by blood clot in the FTCD should be noted by surgeons performing MF, and indications for MF should be carefully considered not only for maximizing the postoperative clinical outcome but also minimizing potential complications, such as formation of subchondral bone cysts or intralesional osteophytes.