Among the first issues he will have to deal with is superstar Ronaldo -- who he bought in 2009 from Manchester United.
"As no other candidature was put forward to the board ... it is proclaimed that Mr Florentino Pérez Rodríguez is president of Real Madrid," the Spanish and European champions said in a statement.
The 70-year-old construction magnate's third term in charge of Europe's most successful club spanning 15 years -- 2000-2006 and since 2009 -- will be rubber stamped at a ceremony at the Santiago-Bernabéu Stadium later Monday.
And among the first issues he will have to deal with is superstar Ronaldo -- who he bought in 2009 from Manchester United for a record 94 million euros ($105.3 million).
Ronaldo is threatening to leave Spain after running into problems with tax authorities.
The frenzy of speculation began soon after Ronaldo was accused last week of a 14.7 million euro tax evasion through offshore companies.
The Portuguese international is currently in Russia competing for the European champions in the Confederations Cup.
And according to Spanish sports daily Marca, Ronaldo has told his teammates: "I'm leaving Real. I have made a decision. There is no turning back."
Portuguese sports daily A Bola also claimed that Perez had already been informed of the 32-year-old's decision.
There has been speculation that Ronaldo is trying to put pressure on Real so that they will bear some of the burden of an eventual fine as Barcelona did for Lionel Messi.
Among the clubs reported to be interested in Ronaldo is former club Manchester United for a fee which could hit 200 million euros, with a possible get-out clause of one billion euros.
Since extending his contract in November until 2021, Ronaldo is according to Forbes the highest paid sports star in the world with $93 million (83m euro) in 2016-2017.
Paris Saint-Germain, Bayern Munich and Chelsea are also reported to be interested.
Under Perez, Real Madrid have won three Champions League titles in four seasons. The club -- which also won La Liga last season -- lead the way in the elite European competition with 12 trophies.
Perez's opponents have criticised reforms in the club statutes which have toughened criteria for aspiring candidates.
Candidates must now have been a member of Real for over 20 years, compared to the old requirement of 10 years, and have a personal fortune of over 75 million euros.