The aircraft was modified at the company's Wichita, Kan., facility for troop and cargo transport missions.
Boeing and Navy representatives marked the milestone with a ceremonial "passing of the key" at the Wichita facility before the aircraft departed for its home base at Naval Air Station North Island.
"The C-40A combines Boeing commercial airplanes' best-selling 737 with Boeing Defense, Space and Security's modification expertise," said Steve Wade, general manager of Boeing Global Transport and Executive Systems.
"This aircraft increases the Navy's capability for rapid response worldwide and we're looking forward to continuing to enhance the fleet with as many aircraft as the Navy requires."
"The global reach and persistent presence of forward-stationed and rotational naval forces is made possible by Navy Unique Fleet Essential Airlift, and the fuel-efficient C-40A delivers this important capability reliably and at a lower cost," said Rear Adm. Bryan Cutchen, deputy chief of Navy Reserve.
"This new aircraft will help the Navy meet our current challenges today and helps us build a relevant and capable future force."