Third molars are frequently absent or impacted; their unpredictable prevalence and morphology, with frequent anatomical variations, is a challenge for the practitioner. The number of roots of the upper third molars vary from one to five, but five roots upper third molars’ cases are extremely rare. The case reported here is of a normotrophic male patient, with no significant general medical history, having extracted an impacted maxillary upper molar, with an unusual position and dimensions and five completely separated formed roots, orientated in diverse directions. It highlights the importance of using the correct surgical technique, without excessive pressure, for avoiding the fracture of the maxillary tuberosity, the displacement of the molar into the pterygopalatine fossa or the opening of the maxillary sinus, especially in the absence of good quality imagistic information like cone-beam computed tomography. The case presented in this paper is very rare and highlights the significance of anatomical knowledge, which is mandatory for managing these cases, to avoid trauma, accidents, and complications and to maintain an optimal time of extraction, since such variations occur, and the conventional radiographs do not offer enough data to clarify the diagnosis.