In his professional debut on March 25, 1997, Vargas crushed Jorge Morales in just 56 seconds. Immediately, a star was born. Fernando blasted his next five opponents all within two rounds, eliminating four of his five challengers in one round each. After six professional bouts, Vargas had fought a total of only eight rounds. Vargas racked up an impressive record of 14 victories with 14 KOs against no defeats by the time he fought for his first world championship.

Vargas won his first world title in 1998, knocking out Yori Boy Campas in seven rounds for the IBF light middleweight championship, becoming the youngest champion in the light middleweight division's history [21 years and 5 months]. Vargas successfully defended the title throughout 1999, with victories over Howard Clarke (TKO 4), Raúl Márquez (TKO 11), Winky Wright (MD 12), and Ike Quartey (UD 12).

Vargas is arguably 3-time Junior Middle Weight Champion of the World.