The 70-year-old, who is in his second spell as president, stood unopposed for the post.
Perez held the position for the first time between 2000 and 2006, a period during which Real signed Luis Figo, David Beckham and Ronaldo.
He returned in 2009, as the club bought Cristiano Ronaldo, Kaka, Karim Benzema and Xabi Alonso.
Cristiano Ronaldo's future at the Bernabeu remains uncertain after he told the club he wants to leave.
Perez employed six managers during his first spell, as Real won two La Liga titles and the Champions League.
He resigned in February 2006 after the club went three years without a major trophy.
Last season, Real Madrid became the first side to retain the Champions League and won the Spanish title for the first time since 2012.
Florentino Perez will continue as Real Madrid president after being re-elected for the next four years.