After politics
In the 1990s, Stephenson was appointed as a board member on the province's new Education Quality and Accountability Office, which monitors and reports to the public on the performance of the education system. From 1997 to 2005, she was chair of the Learning Opportunities Task Force. and was involved with the Gwillimbury Foundation in its attempt to build a university in Queensville, Ontario. She is a founding member of the Canadian Institute for Advanced Research and also served on the boards of the Ontario Innovation Trust and the police services board overseeing the Ontario Provincial Police. In 1999, she was awarded the Order of Ontario and the Governor General's Award in Commemoration of the Persons Case. The Bette Stephenson Centre for Learning, a York Region District School Board school in Richmond Hill offering adult education programs, was named after her. In 2013, she was inducted into the Canadian Medical Hall of Fame.
Stephenson died in Richmond Hill on August 19, 2019, at the age of 95.