Diaphragmatic endometriosis is rare and forms 0.67–4.7% of all endometriosis cases. Evidence regarding its optimal management is lacking. In this study, we retrospectively analyzed the patient characteristics and long-term treatment outcomes of diaphragmatic endometriosis patients. Over a 4-year period, 23 patients were diagnosed with diaphragmatic endometriosis. The majority of patients had coexisting deep pelvic endometriosis. Cyclic upper abdominal pain was reported by 60.9% of patients, while cyclic chest and shoulder pain were reported by 43.5% and 34.8% of patients, respectively. Most patients were treated with laparoscopic lesion ablation, while 21.1% were treated with minimally invasive excision. The mean follow-up time was 23.7 months. Long-lasting resolution of the chest, abdominal, and shoulder pain occurred in 50%, 35.7%, and 25% of patients, respectively. Nonetheless, 78.9% of patients reported major improvement in their symptoms postoperatively. Significantly higher rates of postoperative shoulder, abdominal, and chest pain were observed in patients who received postoperative hormonal therapy compared with those who did not. All patients treated expectantly remained stable. Therefore, we recommend treating diaphragmatic endometriosis only in symptomatic patients. The risk of incomplete surgery should be minimized by a multidisciplinary diagnostic and therapeutic approach with a careful assessment of the diaphragm and the thoracic cavity.