In 1993, Hughes was named HSL-44 (now HSM-74) Pilot of the Year and was the co-recipient of the Commanding Officer's Helmsman Award.[3] Hughes served as the flag lieutenant to commander for Carrier Group 4 on all six East Coast aircraft carriers.[3] He then served as the executive officer and the 14th commanding officer of the Fighting Vipers of HSL-48 (now HSM-48).[3] In 2007, he received the Helicopter Maritime Strike Wing, United States Atlantic Fleet Navy and Marine Association peer-selected leadership award.[3] He also served as the commander, Helicopter Maritime Strike Wing, United States Pacific Fleet.[3] In his first flag assignment, he served as the commander, Navy Recruiting Command. On July 21, 2017, he was appointed as commander of Expeditionary Strike Group 2.[3]
In March 2018, Hughes assumed command of Navy Personnel Command and became Deputy Chief of Naval Personnel.[8] On November 12, 2020, he was nominated for promotion to vice admiral[9] and assignment as Deputy Chief of Naval Operations for Warfighting Development.[10] On December 14, 2020, his nomination was confirmed by voice vote of the full United States Senate.[9] In May 2023, he was nominated for assignment as the deputy chief of staff for capability development of Allied Command Transformation.[11][12]