After his coaching career ended, UCLA continued to honor Wooden with the title of Head Men's Basketball Coach Emeritus. On November 17, 2006, Wooden was recognized for his impact on college basketball as a member of the founding class of the National Collegiate Basketball Hall of Fame. He was one of five people—along with Oscar Robertson, Bill Russell, Dean Smith and Dr. James Naismith—who were selected to represent the inaugural class. In 2009, he was inducted into the Missouri Valley Conference Athletics Hall of Fame in St. Louis. Coach Wooden was the ninth honoree in the Missouri Valley Conference's Lifetime Achievement category. Wooden said the honor he was most proud of was "Outstanding Basketball Coach of the U.S." by his denomination, the Christian Church.
On Wooden's 96th birthday in 2006, a post office in Reseda, California, near where Wooden's daughter lives, was renamed the Coach John Wooden Post Office. This act was signed by President George W. Bush based on legislation introduced by Congressman Brad Sherman.
Wooden was in good physical health until the later years of his life. On April 3, 2006, he spent three days in a Los Angeles hospital, receiving treatment for diverticulitis. He was hospitalized again in 2007 for bleeding in the colon, with his daughter quoted as saying her father was "doing well" upon his subsequent release. Wooden was hospitalized on March 1, 2008, after a fall in his home. He broke his left wrist and his collarbone in the fall, but remained in good condition according to his daughter and was given around-the-clock supervision. In February 2009, he was hospitalized for four weeks with pneumonia.