He was named interim head coach before the 2011 season, after Dan Callahan died.
Henderson had also served as interim head coach for the final 20 games of the 1994 season.
He was credited by Collegiate Baseball with assembling a highly ranked class in 1987.
In 1991, he arrived at Southern Illinois, and added associate head coach duties in 1993.
He coached 35 players at SIU who went on to be drafted, including Jerry Hairston Jr. and Jason Frasor.