 Flagler was selected by the San Francisco 49ers in the first round (25th overall) of the 1987 NFL Draft.In three years he only had 42 carries for 145 yards and one touchdown, while playing behind Roger Craig.After asking for a trade, he was sent along with Daniel Stubbs, a third (#81-Craig Veasey) and an eleventh-round (#304-Myron Jones) draft pick to the Dallas Cowboys, in exchange for a second (#47-Dennis Brown) and third-round (#68-Ron Lewis) draft choices on April 19, 1990.