McGaughey won his first Travers Stakes, the summer classic of US racing with Easy Goer in 1989. He followed with Rhythm in 1990 and Coronado's Quest in 1998 but then had to wait 21 years for Code Of Honour to make it four.
Raced by Lane's End's Wiliam S Farish Code of Honor, a 4/1 shot, stormed to the lead in deep stretch for an authoritative 2.5 lengths victory.
Favorite Tacitus and Bob Baffert's West Coast raider Mucho Gusto vied for the lead early but the two pacesetters had no answer when Code Of Honor made his move.
Tacitus battled gamely for second with Mucho Gusto as the winner recorded 2.01.05 for the 1 1/4 miles.
Code of Honor won the G2 Fountain of Youth Stakes in March and was third in the G1 Florida Derby before he tackled the G1 Kentucky Derby where he was promoted to second after the disqualification for first past the post Maximum Security.
He most recently recorded a 3.25 lengths win in the G3 Dwyer Stakes at Belmont on July 6.
McGaughey said the Travers win justified his decision to bypass the Preakness Stakes and Belmont Stakes with Code Of Honour.
"Unless we won the Derby I wasn't going to run him in the Preakness or the Belmont," he said.
"He had time between races and he's done everything right. I think he's done nothing but move forward."
The Saratoga meeting is one of the biggest days of the year in US racing and featured an four G1 races – the Ballerina Stakes, Personal Ensign, Forego Stakes and Sword Dancer Stakes.