A native of Miami, Florida, Howser grew up in West Palm Beach, Florida; graduated from Palm Beach High School; and attended college at Florida State University. He was a member of the Sigma Nu fraternity. At Florida State, he received honors twice as an All-American shortstop and set a school record with a batting average of .422 in 1956. Signed by the Kansas City Athletics, he hit .280, stole 37 bases, scored 108 runs, and led American League shortstops in putouts and errors in his rookie season. For this he was selected to the 1961 All-Star team, and was named "The Sporting News" rookie of the year.