Bone-tendon junction (BTJ) overuse injuries are common athletic and occupational problems. BTJ injuries may sometimes be caused by resuming training too early after injury. To study the effects of post-injury resuming training within 48 hours on the acute injury healing process, as it is often the case for athletes. Twelve mature female rabbits were assigned to one of the following groups: acute injury (AI, n = 6), post-injury early return to training (PIERT, n = 6) and normal control (CON, n = 6). Tissue specimens were harvested at week 4. The radiological and histological characteristics of the AI and PIERT groups were compared among the groups. The trabecular thickness of the PIERT group was significantly different from those of the AI and CON group. A histological evaluation revealed poor collagen fibre alignment, extensive scar tissue and lowered cell density in the AI and PIERT groups compared with the CON group, but no significant differences were observed between the AI group and the PIERT group. The fibrocartilage zone and proteoglycan area in the PIERT group were significantly different from those in AI group. No differences were observed in the Total VOI volume (TV), Object volume (OBV), Percent object volume (BV/TV) and trabecular number (Tb.N) among the AI, PIERT and CON groups. In conclusion, a repeatable animal model of bone-tendon junction acute micro-damage by puncture was established. Resuming training in 48 hours did not significantly deteriorate the BTJ injury healing, but improved bone remodelling and increased fibrocartilage zone thickness.