He played college baseball at Linfield in 1980 and at San Diego State for head coach Jim Dietz from 1982 to 1984.
[4] Henderson pitched one year at Linfield College before transferring to San Diego State University, compiling a 19–5 career record at the two schools.
Following a trip to the 1996 College World Series, he was named the National Assistant Coach of the Year by Collegiate Baseball newspaper.
After a successful stay at Florida, he moved back to the west coast as an assistant coach at Oregon State.
In February 2018, Henderson was named interim head coach at Mississippi State after Andy Cannizaro resigned due to off the field indiscretions.