Ellis was selected by the New York Jets in the first round with the 12th overall pick in the 2000 NFL Draft. He was the first of four first round draft picks that the Jets had that year, and was the compensation pick from the New England Patriots for hiring Bill Belichick away from the Jets as their head coach. The other players drafted were defensive end John Abraham (13th overall), quarterback Chad Pennington (18th overall), and tight end Anthony Becht (27th overall).