Deep benign fibrous histiocytoma (FH) is an uncommon and poorly recognized tumor that arises in subcutaneous or deep soft tissue. Deep benign FH of the trachea is even more rare. Deep benign FH recurs in approximately 20% of cases, so surgical resection is the recommended treatment for FH. However, some patients are afraid of the trauma and potential complications from the resection of tracheal tumors, so they do not accept surgical resection. With the development of interventional pulmonology, bronchoscopic intervention plays a key role in the treatment of benign tracheal tumors. Novel tools have emerged in interventional pulmonology and optimized the traditional techniques. Here, we report a case of deep benign FH of the trachea with broad base relapse after electrocautery with snare, argon plasma coagulation (APC) and radiotherapy. It was treated successfully by endobronchial resection with a hybrid knife (HK) and APC. The HK is a hybrid device that combines an electrocautery knife with a water jet in one instrument. Submucosal injection and circumferential cutting and dissection of lesions as well as coagulation of bleeding can be performed only with the HK. During the 6 months follow-up, the deep benign FH of the trachea did not relapse. In the case reported herein, the HK enabled submucosal injection and circumferential cutting and dissection of lesions as well as access to submucosal lesions to gain further adequate APC treatment, thereby allowing a better clinical response than that achieved by traditional electrocautery with snare and APC. In conclusion, the HK with a water jet is a feasible and effective endoscopic method for management for benign or low-grade malignant neoplasms of the trachea, especially those with a wide base and submucosal involvement.