MATLAB was created in the 1970s by Cleve Moler, who was chairman of the computer science department at the University of New Mexico at the time.

In 1999, the U.S. Department of Justice filed a lawsuit against MathWorks and Wind River Systems alleging that an agreement between them violated antitrust laws.

The agreement in question stipulated that the two companies agreed to stop competing in the field of dynamic control system design software, with MathWorks alone selling Wind River's MATRIXx Software and that Wind River would stop all research and development and sales in that field.

[16] MathWorks's Simulink software was found to have infringed 3 patents from National Instruments related to data flow diagrams in 2003, a decision which was confirmed by a court of appeal in 2004.

[21] The logo represents the first vibrational mode of a thin L-shaped membrane, clamped at the edges, and governed by the wave equation, which was the subject of Moler's thesis.

[24] The company actively supports numerous academic institutions to advance STEM education (primarily through the use of MathWorks products), including giving funding to MIT Open Courseware and MITx.