In June 2009, President Barack Obama nominated McHugh to the position of United States Secretary of the Army.

This part of Upstate New York has historically been very Republican at the congressional level, though it has recently become more competitive in presidential elections.

[5] McHugh was a member of the board of directors of the United States Military Academy in West Point, New York for 14 years, including a term as chairman.

He was chairman of the Oversight Committee's Post Service Subcommittee for six years, and worked to pass legislation to significantly reform the U.S.

[7] At the time, Johnson speculated that he was added to the list because of his anti-war views and opposition to McHugh.

A later CBS News investigation discovered that the name "Robert Johnson" appeared on the list due to its use as an alias by a man convicted of plotting bombings in Toronto.

[11] On June 2, 2009, McHugh was nominated to the position of Secretary of the Army, by President Barack Obama.

[18] In May 2010, McHugh was granted an honorary degree from the State University of New York Board of Trustees, to be presented during the commencement ceremonies at SUNY Oswego.

When the decision to award McHugh the honorary degree was made public, the SUNY Oswego Pride Alliance, an LGBT student group, organized a protest to be held on campus during the ceremony, with students specifically taking issue with his voting record on gay rights.

"[19] In March 2015, McHugh revoked a rule allowing Women Airforce Service Pilots (WASPs) to have their ashes interred at Arlington National Cemetery, ruling these women lacked eligibility due to their classification during the war as civilians.

At the time of the announcement defense secretary Ashton Carter and senior New York senator Charles Schumer expressed praise and appreciation for McHugh's service.

[24] On October 23, 2015 the Army conducted a farewell ceremony for McHugh, which was presided over by Secretary of Defense Ashton Carter.

During the ceremony McHugh was presented with the Department of Defense Medal for Distinguished Public Service.