In 1986, Ware signed with the World Wrestling Federation, where he debuted his fun-loving "Birdman" persona, complete with a macaw named "Frankie". Ware made his debut as a fan favorite on the September 6, 1986, episode of Superstars, teaming with Paul Roma against the Hart Foundation (Bret Hart and Jim Neidhart) in a losing effort. His first victory was on the September 7 episode of Wrestling Challenge against Bob Bradley. He made his entrances dancing to the ring to the tune of "The Bird", flapping his arms and carrying Frankie, who sat on a perch at ringside while Ware wrestled. Bright outfits, colorful sunglasses, a constant smile and his vibrato singing voice made Ware popular, especially with the younger crowd that the WWF mainly catered to during the 1980s. Ware also sang the title track of the 1987 WWF album Piledriver, which then became his entrance music.
Ware garnered his first big win of his initial WWF run when he upset Harley Race at a house show in East Rutherford, NJ, on October 13. On television, his first major showcase was at the November 29, 1986 Saturday Night's Main Event VIII where he defeated Nikolai Volkoff. He was then granted an Intercontinental Title match against champion Randy Savage on the November 16 edition of WWF Superstars, a bout which went to a double countout. The same taping later saw Ware defeat Savage by countout in a dark match.
Ware, however, would often be on the losing end when he came up against other established stars, stars as Butch Reed, Hercules, Greg Valentine, and The Big Boss Man. From 1987 to 1993, Ware appeared on several WWF PPVs (including WrestleMania III where he lost to Reed) and editions of Saturday Night's Main Event, being used mainly to make established or rising stars look good. Ware was the first wrestler on television to fall victim to the Perfect-plex of newcomer Mr. Perfect on the January 7, 1989, episode of Saturday Night's Main Event XIX, while at the 1990 Survivor Series, Ware became the first wrestler to fall victim to The Undertaker's Tombstone piledriver in the Undertaker's WWF debut match. During a 1989 European tour, Ware was released.
In 1992, Ware teamed up with Owen Hart to form the high flying team known as High Energy, well known for their gigantic baggy brightly colored pants and checkered suspenders. High Energy feuded with (and generally lost to) The Nasty Boys, The Headshrinkers, and Money Inc.. They made only one pay-per-view appearance as a team, a loss to the Headshrinkers at the 1992 Survivor Series. Ware appeared in the first match on the very first episode of Monday Night Raw on January 11, 1993 where he was defeated in a squash match by Yokozuna. The team ended in March 1993 after Hart injured his knee. High Energy's final match came in a loss to The Headshrinkers at a live event on March 10.
With Owen Hart out of action, Koko would return to singles competition and immediately entered a house show series with Skinner.
Koko returned to WWF in 1994 when he appeared on the March 21 episode of Monday Night Raw and faced Jeff Jarrett. He would then appear on the April 9 episode of Superstars in a loss to Irwin R. Schyster. Koko picked up his first victory of his return by defeating Bastion Booger on the April 16, 1994 episode of WWF Mania. Koko then embarked on a house show tour in England where he faced Jarrett and Kwang. On May 19, he defeated The Genius and followed it up a night later with three more wins over Poffo later that month. Koko faced his former partner Owen Hart on the June 18 episode of Superstars. He ended his WWF run with three straight victories as he teamed with Bushwhacker Luke in house show matches in the Philippines, Hong Kong, and Singapore against Reno Riggins and Barry Horowitz.
In 1999, Ware made a short-lived return to the World Wrestling Federation where he put on the "Blue Blazer" mask during the Owen Hart angle. When Hart died, the angle was dropped and Ware's services were no longer needed.
He also appeared at "WWE Homecoming", Raw's return to the USA Network, on October 3, 2005. He fought (and was defeated by) Rob Conway on the October 28, 2005 edition of WWE Heat.
On April 4, 2009, Ware was inducted into the WWE Hall of Fame by The Honky Tonk Man.