Most of his career was spent at Lipscomb in Tennessee and Northern State in South Dakota.
Meyer died at his home in Aberdeen, S.D., at 6:52 a.m., according to family spokeswoman Brenda Dreyer.
"He won his greatest victory and is now running again and gearing up to pitch nine innings," the Meyer family said in a statement. "The family appreciates the outpouring of love, prayers and concern."
Meyer kept coaching after being critically injured in a traffic accident in September 2008. He endured several operations, which included removing his spleen, repairing cracked ribs and having his left leg amputated below the knee.
Meyer later called the accident a blessing because doctors found cancer in his liver and small intestines during the operations.
Four months later, while in a wheelchair, he became the winningest men's coach on Jan. 10, 2009.
Meyer was honored in July 2009 with ESPN's Jimmy V Perseverance Award, given to a sports figure who has overcome great obstacles. The award is named after former North Carolina State coach Jimmy Valvano, who died of cancer in 1993. Meyer was also awarded the John W. Bunn Lifetime Achievement Award from the Naismith Memorial Basketball Hall of Fame in August 2010.
Meyer had other health issues in recent years. He had surgery in August 2012 for a heart pacemaker implant. That occurred after having three of his heart valves replaced with mechanical ones. He also had a hole in his heart repaired.