The 57-year-old head of one of Spain's largest construction companies gained the support of 94.25 percent of the 30,151 club members who cast their votes on Sunday for the three candidates standing in the election to ensure himself of a second term as president.
Former president Lorenzo Sanz polled just 4.05 percent of the votes and the third candidate Arturo Baldasano gained 1.7 percent.
Perez polled 55 percent of the votes cast when he defeated Sanz in July 2000.
Overall 47.56 percent of the 65,197 members who were entitled to vote took part in the election, a lower turn out than the last poll.
"The voice of the Real Madrid members has been expressed clearly and emphatically," Perez told supporters at his electoral headquarters after the results were announced.
"Today Real Madrid has won and the future has won. I know what challenges I face after this victory and I take on this responsibility in the knowledge that the only limits of Real Madrid are the dreams of it members."
RESOUNDING ENDORSEMENT
The victory was a resounding endorsement of Perez's four-year reign in charge of one of Europe's most powerful football clubs.
Real members clearly decided that despite the team's disappointments on the pitch last season during which they failed to win a trophy for the first time in five years, Perez was still the best man to lead the club.
Although his rivals argued that Real is still heavily in debt, Perez said he had solved the club's financial problems as a result of the sale of its city-centre training ground and improved marketing.
He also made much of his ability to bring the leading names in world football such as Ronaldo, Zinedine Zidane and David Beckham to Real during his first term in charge at the club.
So far he has made no promises about which players he might sign, but he has said he has been negotiating with European champions Porto to bring in defender Ricardo Carvalho and midfielder Costinha.
He has, however, pledged to continue recruiting the world's top players to the club and has hinted that he will try and sign another "galactico" before the start of next season.
Off the pitch, Perez's election programme included plans for the construction of a $36 million (19.4 million pounds) retractable roof for the club's Bernabeu stadium and the completion of a state-of-the-art training facility close to Madrid's Barajas airport.
