His professional career began on March 25, 1988, when he beat Efren Chavez by a knockout in round four in Irvine, California. He won eight fights that year, five by knockout, of which four were in the first round. In 1989, he won seven more fights, including a first round knockout of Abner Barajas and an eight round decision against John Michael Johnson.
In 1990, he kept his winning ways, winning seven more bouts, including an eight round decision over Jesus Chong, an 11th round technical knockout of Roland Gomez in Reno that gave him the United States Junior Bantamweight title, and a twelve round decision over Luigi Camputaro, to retain that title. Tapia was, by the end of the year, becoming a known boxer, his name often appearing on magazine articles. He also has a nephew currently going to school named Michael Tapia attending Justin-Siena High School.
But his career took an enormous step backwards when he was found with drugs, and this time he was suspended from boxing for three years. He had to start over from scratch when he was finally able to return in 1994.
When he was finally back in the ring, he beat Jaime Olvera by a knockout in four rounds at Tulsa, Oklahoma. He won three more fights by knockout, and then he faced Oscar Aguilar at the Michael Carbajal-Josue Camacho undercard in Phoenix for the NABF Jr. Bantamweight title. He won that fight by a knockout in the third round. After that fight, Albuquerque Police claimed they found cocaine in a bag carried by Johnny five days later. Johnny claimed what the police found was only a soap bar, and then charges were eventually dropped. He defended the title twice before the year was over, with an eleventh round knockout of Henry Martinez and a second round knockout of former champion Rolando Bohol.
On February 18, 1995, Tapia was given a shot at WBO World Junior Bantamweight champion Jose Rafael Sosa. Tapia became a world champion in his own hometown by defeating Sosa on a twelve round decision.
He retained the title with a nine round technical draw with Ricardo Vargas and a decision in twelve against former amateur nemesis Arthur Johnson. After two more wins, he gave Willy Salazar a title shot, knocking him out in nine rounds.
1997 saw Tapia fend off a challenge from Marco Antonio Barrera's brother Jorge Barrera, in three rounds. After that, the fight with Romero was set for Las Vegas. The fight took place on July 18, the only related trouble was when a Southwest Airlines plane, carrying as passengers two members of the gangs the boxers were related to, reported an attempt to fight by those passengers. However riot police in Albuquerque were on alert the whole fight weekend. Tapia won by a unanimous twelve round decision, to add the IBF world title to his own WBO belt. In his next fight, he defended the belts in Florida against Puerto Rico's Andy Agosto, also by decision in twelve.
In 1999, Tapia suffered his first loss, losing a twelve round decision and the WBA world title belt to Paulie Ayala in what Ring Magazine called its "fight of the year." That year also, he tried to commit suicide with a drug overdose, and required hospitalization. Back quickly after that and his first defeat, he was given a chance at the WBO world title belt, and he became a two time World Bantamweight champion by beating Jorge Eliecer Julio by a decision in twelve at Albuquerque on January 8, 2000. After defending his belt with a twelve round decision over Javier Torres, a rematch to unify the belt between Ayala and him was set up. In what became another candidate for "fight of the year," Ayala edged out another close, split decision win. Tapia then went back home to prepare for his upcoming bouts in 2001, when he went up in weight and beat Famosito Gomez by a knockout in six, and former World Featherweight champion Cesar Soto by a knockout in three.
Tapia has had many tattoos done around his body, and his tattoos are prominent when he is fighting. One of them says Mi Vida Loca ("My Crazy Life"), the nickname he has adopted over the last few years. He wrote an autobiography by that title.
He is now a born-again Christian and currently holds a record of 55 wins, 5 losses, and 2 draws, with 28 wins by knockout.
Tapia was arrested in Bullhead City, Arizona the night of January 10, 2003 for resisting arrest along with his cousin, who was wanted on charges in New Mexico. He was not sent to jail immediately, but now he faces new charges for resisting arrest. After his arrest, he returned home to Las Vegas, and there, he slipped onto the floor, crashing his head against the concrete and having to be hospitalized in critical condition. He recuperated and was later released.
At 38 years-old, Johnny Tapia faced the little known Mexican, Sandro Marcos, in Chicago. In the second round, Marcos connected with a left-hook to the body. Tapia fell to the canvas, clutching his ribcage, as referee Genaro Rodriguez reached the count of 10.
Tapia was found unconscious and not breathing in a hotel room early on the morning of March 12, 2007. Tapia was hospitalized in critical condition from an apparent cocaine overdose at Albuquerque Presbyterian Hospital.
The next day, on the morning of March 13, Tapia's brother-in-law and nephew were killed in an automobile accident on U.S. Highway 550 near Bloomfield, NM, apparently en route to the hospital to visit Tapia. That same day, Tapia was upgraded from critical to serious condition.