This report describes the management of an uncommon case of dens invaginatus of a microdontic upper lateral incisor, with an extended apical lesion. Dens invaginatus is a developmental abnormality of a tooth where enamel and dentin fold into the pulpal space. This abnormal anatomy, and the separation of two distinct root canal spaces, complicates conventional treatment, making the apical portion inaccessible to instrumentation and impeding disinfection of the canal space. The coexistence of dens invaginatus affecting a microdontic tooth is a rare anomaly found in the literature. This case report describes a young female patient with dens invaginatus affecting a microdontic maxillary lateral incisor, combined with necrotic pulp and apical periodontitis. The conventional treatment was completed first to disinfect the coronal portion of the accessible pulpal space. At a subsequent appointment, it was completed by a surgical approach to cleanse and seal the apical part of the root canal space. The tooth was then restored, and the orthodontic treatment was initiated. One-year follow-up demonstrated a complete healing of the apical lesion.