Three rooted lower first permanent molar represents one of the main anatomical variants which is a treatment challenge of clinicians. This study is aimed at presenting a case of a lower first molar with an additional root that was diagnosed and managed successfully using new techniques in endodontics. Tooth #46 was diagnosed as a necrotic pulp with symptomatic apical periodontitis. Different angle radiographs were obtained, and they clearly showed three roots. The procedure was completed under magnification and illumination using an operating microscope. The access cavity was modified to achieve straight line access for all the canals. Careful step-by-step instrumentation was performed using flexible NiTi rotary files. The canals were irrigated using 6% sodium hypochlorite. Afterwards, three-dimensional obturation was completed using warm vertical compaction. Knowledge of the anatomy and an early diagnosis are required to achieve high-quality root canal treatment.