The Mu Alpha Theta National High School and Junior College Mathematics Club were founded in 1957 by Dr. and Mrs. Richard V. Andree at the University of Oklahoma. The name Mu Alpha Theta was constructed from the Greek lettering for the phonemes m, a, and th.

Pi Mu Epsilon, the National Collegiate Honor Society of Mathematics, contributed funds for the organization's initial expenses; the University of Oklahoma provided space, clerical help, and technical assistance.

 Currently, more than 100,000 students are Mu Alpha Theta members at more than 2,420 schools in the United States and in 23 foreign countries.

The official journal of Mu Alpha Theta, The Mathematical Log, was first issued in 1957 on a mimeograph and was in printed form starting in 1958. It was published four times during the school year until 2002 and featured articles, reports, news, and problems for students.

The first Mu Alpha Theta National Convention was held at Trinity University in San Antonio, Texas in 1968. Each year the convention brings together hundreds of teachers and students from across the country for five days of math-related events. The National Convention rotates among our chapters and has been held in locations all over the country, including Honolulu, Washington D.C., Seattle, Dallas, and Boston.

In 1981, The Kalin Award was initiated to reward outstanding students. The Huneke Award and the Sister Scholastica Award followed in 1986 and 1995 to recognize outstanding chapter sponsors. In 1987, The Andree Award was created to encourage students who plan to become mathematics teachers. In 2002, Mu Alpha Theta offered the Vector Scholars Program to recognize and reward students for outstanding efforts in mathematics and math education. 

In 2004, The Rubin Award was initiated to reward a chapter that has shown a history of outstanding service to its community for at least two years with a mathematics project.

Two years later, the organization began offering merit scholarships to outstanding members. The Regional Sponsor Awards were established in 2015 to celebrate our wonderful sponsors, who devote their time to making Mu Alpha Theta a success at their school. In the summer of 2015, the Governing Council added the Governor's Award for Leadership and Service, an additional student award. 

By 2018, Mu Alpha Theta and the Mu Alpha Theta Educational Foundation awarded more than $316,000 in scholarships, grants, and awards.