Since nanofat is considered one of the richest sources of adipose-derived stem cells with an increased need for new biological approaches for managing temporomandibular joint internal derangement (TMJ-ID) symptoms that impair a patient’s lifestyle, this study evaluated the effectiveness of autogenous nanofat intra-articular injection in managing ID symptoms regarding pain, mouth opening, and joint sound. Furthermore, to assess the consequences and complications of this procedure, 20 patients with 38 TMJs with varying stages of Wilkes classification were included in the study. All involved patients were previously diagnosed with ID depending on a clinical and radiographical basis and had no previous response to conservative management for at least 4 to 6 months. Evaluation of the ID in the preoperative phase, as well as 2 weeks, 1 month, 3 months, and 6 months postoperatively. An evaluation was done depending on pain assessment using a visual analog scale (VAS), measuring maximum mouth opening (MMO) and joint noise if it was present or absent preoperatively and postoperatively. The results show improvement in the symptoms in all follow-up appointments since the VAS of pain decreased significantly with increased MMO and the absence of clicking in most cases during follow-up appointments. We conclude from this study that nanofat intra-articular injection was influential in managing ID symptoms and was safe without significant side effects.