This retrospective study aimed to investigate whether the corono-apical location of sinus tracts differs according to the presence/location of vertical root fracture (VRF) in microsurgically treated root-filled teeth. The cases included were (1) anterior and premolar teeth without a preoperative diagnosis of VRF, (2) those with a periodontal probing depth of ≤3 mm, and (3) those for which preoperative cone-beam computed tomography (CBCT) scans and intraoperative video records were available. VRF was diagnosed intraoperatively. The locations of buccal cortical bone defects and fracture lines were categorized on video images, and the corono-apical sinus tract locations were determined by superimposing video images onto volume-rendered CBCT images. Eleven of the 78 teeth investigated had VRF, and there was no significant difference in the incidence of sinus tracts between vertically fractured and non-fractured teeth (Mann-Whitney U-test, P > 0.05). The location of the sinus tract was significantly more coronal in vertically fractured than in non-fractured teeth (Mann-Whitney U-test, P < 0.0001). The location of sinus tracts was high correlated with cortical bone defects (Spearman’s correlation, P < 0.0001). In microsurgically treated anterior and premolar teeth with a normal probing depth, sinus tracts were located more coronally in vertically fractured than in non-fractured teeth, and were highly correlated with the location of cortical bone defects.