An electronic device including an electronic pen and a method of controlling a communication connection with the electronic pen is provided. The electronic device include a housing, a touch-screen display, a first wireless communication circuit, an extended recess disposed inside the housing, a first wireless charging circuit; an electronic pen including a second wireless communication circuit and a second wireless charging circuit electrically coupled to the first wireless charging circuit, a processor, and a memory. The memory stores instructions causing the processor to detect whether the electronic pen is inserted into the recess, charge the electronic pen through the first wireless charging circuit based on the detection, receive inherent information of the electronic pen through the first wireless communication circuit during or after the charging, and maintain or re-establish a communication connection with the electronic pen based on at least a portion of the received inherent information.