The museum presents exhibits and quality educational programs that convey the diversity of individuals and events that shape the historical and technical context of the nuclear age.

In January 2005, NAMF asked DOE/NNSA (National Nuclear Security Administration) for 12 acres (4.9 ha) of land at the intersection of Eubank and Southern Boulevards in southeast Albuquerque for construction of a new museum.

The site provides nine acres (3.6 ha) of outdoor space for exhibits of military aircraft, missiles, vehicles, and the sail of the USS James K. Polk nuclear submarine.

Permanent exhibits focus on the following: Pioneers of the Atom – An interactive display that introduces the individuals who questioned and defined the matter which makes up the universe.

World War II – A display that teaches the history leading up to the creation and use of the atomic bomb and the countries that became involved.

Based on scholarly and eyewitness accounts, this exhibit features many artifacts that would have been (or were actually) present at Los Alamos National Laboratory in the 1940s.

These exhibits include a series of displays striving for an objective examination of the history leading up to and the policy decisions regarding the deployment of the first nuclear weapons code-named Little Boy and Fat Man.

The exhibit includes the text of comments by Manhattan Project staff (including a contentious Edward Teller statement advocating a high-altitude night-time demonstration detonation over Tokyo to precipitate Japanese surrender), the text of statements by Japanese politicians and military leaders, a copy of the petition protesting use without warning submitted by nuclear physicist Leó Szilárd, and photographs from the Hiroshima Peace Memorial Museum.

Hiroshima and Nagasaki – This exhibit pays tribute to the people affected by the detonation of the atomic weapons that the Manhattan Project developed.

Cold War – An examination of the strategic conflict between the United States and the USSR in the second half of the 20th century, through US nuclear testing in the Marshall Islands and at the Nevada Test Site, Soviet nuclear development, the October 1962 Cuban Missile Crisis, and leading to the eventual collapse of the Soviet Union.

[14][15] Some people saw the erecting of the rocket in an area of the city frequented by lovers of the arts and families with children as emblematic of pervasive military-industrial complex influence in Albuquerque and New Mexico.

In 2023, Jennifer Hayden became the President and CEO of the NMNSH, replacing Jim Walther, who was executive director of the museum for 26 years.

[26] The Museum conducts year-round primary, secondary, and adult education programs both in-house and via outreach using the Up'n'Atom Mobile.

[27] The museum hosts guest speakers, annual special events, and week-long youth science camps in the summer.