In most of the cystic lesions appearing in the oral cavity, proper diagnosis and treatment remains a challenge. As glandular odontogenic cyst (GOC) is a rare type of developmental odontogenic cyst, it was not included in our differential diagnosis. The report of GOC was quite surprising as it was rare and never came in this discussion. A 25-year-old male patient was reported to our center with a chief complaint of painless swelling in the right anterior region of the maxilla. The swelling was oval shaped and diffuse extending from the distal aspect of 11 to the mesial aspect of 14 and superiorly extending into the sulcus. Working diagnosis was a periapical cyst, so conventional treatment of root canal treatment, cyst enucleation, and apicoectomy was done. This article presents a rare case which was primarily misdiagnosed and treated and has been subsequently revealed histopathologically as a rare clinicopathological entity.