During the 1990's, the academy's future seemed in doubt, as its elimination was recommended by the National Performance Review efforts of the Clinton administration, chaired by then-Vice President Albert Gore Jr.

Most recently, Academy midshipmen and graduates have been involved in many facets of the War in Iraq. Many graduates were involved in the transportation of supplies during the buildup to the war in 2003. Many graduates in the Naval Reserve have been called to serve supporting Naval roles in ports in Iraq and Kuwait. Graduates who have entered other branches of the service have had more direct roles in Iraq. Aaron Seesan, a 2003 graduate and Army Lieutenant, was the first graduate to give his life for his country during a war since Vietnam.

Due to the service of Midshipmen in every major conflict the country has been involved in since World War II, the regiment is privileged to carry a regimental battle standard. The Merchant Marine Academy is the only Federal Service Academy granted the right to do so, and the standard is carried with the colors at all times. Campaign ribbons from all the conflicts Midshipmen have taken part in help to dress the battle standard, and bring honor to the academy and her midshipmen.

On 19 June 2006, United States President George W. Bush gave the commencement address at the Academy. He used the opportunity to make a major foreign policy initiative on the Iranian nuclear program. He was the first sitting President to visit the Academy, and his address was the first time an American President addressed the Academy