<i>Enterococcus faecalis </i>was the main causative bacteria of refractory periapical periodontitis (PP), there is a pressing need to explore effective methods for eradicating <i>E. faecalis </i>in patients with refractory PP. This study aimed to assess the anti-infective effectiveness of phage PEf771 in treating periapical inflammation in rats. We developed a rat model of PP through <i>E. faecalis </i>YN771 induction. Micro-computed tomography and hematoxylin-eosin staining were utilized to evaluate bone destruction and inflammation in experimental teeth for seven consecutive weeks. Subsequently, rats with PP caused by <i>E. faecalis</i> YN771 were treated with phage PEf771, calcium hydroxide preparation, and 2% chlorhexidine gel. The healing progress of bone defects and inflammation in the apical region was monitored over three consecutive weeks using imaging and histopathology assessments. The PP rat model was successfully developed, and bone destruction and inflammatory cell infiltration in the apical region of the experimental tooth peaked at 4 weeks. The area of bone destruction in rats treated with phage PEf771, calcium hydroxide preparation, and 2% chlorhexidine gel was significantly smaller than that in the untreated group. Phage PEf771, calcium hydroxide preparation, and 2% chlorhexi-dine gel all have the effect of promoting the healing of apical lesions. Therapeutic effects of phage PEf771 on periapical inflammation infected by <i>E. faecalis </i>YN771 enhanced with time. Phage PEf771 promoted the healing of apical lesions, presenting a promising new approach for the treatment of refractory PP using bacteriophages.