Many unanswered questions remain about what constitutes appropriate guidelines for treatment of Merkel cell carcinoma (MCC). In this review, we address current uncertainty surrounding optimal management of Merkel cell carcinoma. These areas of uncertainty include early recognition features; clinical and histopathologic prognostic factors; optimum margins of excision of the primary tumor; indications for and value of surgical staging of the clinically negative regional nodes; optimum management of the patient with pathologically positive regional nodes; and indications for and value of radiation to the primary and regional nodes. Through identifying and elaborating on these areas of uncertainty, the authors hope to foster additional research and ultimately improve the evidence base for future iterations of the NCCN Clinical Practice Guidelines in Oncology in this rare but increasingly encountered cutaneous malignancy. The intent, however, is not to exhaustively identify all areas of controversy, but rather to highlight clinically relevant questions that further studies could address to improve the standard of care for MCC.