The primary maxillary second molars usually have three roots. However, an additional root located mesiopalatally is occasionally observed. This study aimed to determine the relationship between a mesiopalatal root of primary maxillary second molars and an abnormal eruption pattern of maxillary second premolars. The study was performed on cone beam computed tomography images taken from 916 children who visited the Dental Hospital of Kyung Hee University from 2010 to 2018. 744 serial cross-sectional cone beam computed tomography images were evaluated. The overall incidence of the mesiopalatal root of primary maxillary second molars was 3.2% (n = 24) and the abnormal eruption pattern of maxillary second premolars was 19.2% (n = 143). Especially, patients with the mesiopalatal root of primary maxillary second molars were significantly more likely to have the abnormal eruption pattern on maxillary second premolars (p = 0.000). The odds of the abnormal eruption pattern of maxillary second premolars with the mesiopalatal root of primary maxillary second molars was about 13 times higher than those without. The eruption pattern of the permanent successor should be carefully observed and treated if the mesiopalatal root of primary maxillary second molar is existent.