To investigate the effect of increasing the apical size of roots enlarged for root canal obturation on the outcome of non-surgical endodontic treatment for teeth with apical periodontitis. In this retrospective study, we included 210 cases of single-rooted canals treated at our dental units between October 2009 and January 2022. The clinical outcomes of teeth with enlarged root apical size from the International Organization for Standardization standard numbers 25 to 100 were investigated. The number of teeth with a root apical size of ≤50 and ≥ 55 were 158 and 52, respectively. In the former case, 144 (68.6%) teeth had good prognoses and 14 (6.7%) had poor prognoses. In the latter case, 28 (13.3%) teeth had good prognoses and 24 (11.4%) had poor prognoses. Unfavourable clinical outcomes were observed in root canal-filled teeth with an enlarged apical root size of ≥ 55. Thus, these sizes potentially indicate poor outcomes of nonsurgical endodontic treatments.