Algerian and French academics have long campaigned for the return of the 37 skulls, a symbolic hangover from France's 130-year occupation of Algeria.
"We also discussed a number of bilateral issues, including the joint desire to strengthen economic ties ahead of the 4th session of the French-Algerian High-Level Intergovernmental Committee to be held Thursday in Paris", he said. "I am ready", Macron earlier told the Algerian website All About Algeria.
"But from now on, I hope. that we will turn together towards the future".
Macron also held talks with other top Algerian officials, including Prime Minister Ahmed Ouyahia.
He later laid a wreath at a monument in central Algiers to those killed in the war, and walked through the centre of the capital, talking with passers-by.
He told reporters they discussed the USA decision to recognise Jerusalem as Israel's capital, crisis-hit Libya and the anti-terrorism struggle in the Sahel.
"I have acceded to a request, reiterated several times by the Algerian public authorities, for the restoration of the skulls of the Algerian resistance fighters and I took the decision to restore them", he said at a press conference at the end of his friendship and working visit to Algeria.
In a recent trip to west Africa, Macon also called for "neither denial nor repentance", stressing that "we can not remain trapped in the past".
France has praised Algeria's "experience in the fight against terrorism and radicalisation", a reference to its decade-long civil war in the 1990s.
He touched a nerve in Algiers by choosing its regional arch-rival, neighbouring Morocco, for his first visit to the Maghreb.
In his interview with Algerian newspapers, he said: "Algeria must open up more, there are still many obstacles to investment".
"It is also a working visit given the strategic partnership between the two countries".
France's President Emmanuel Macron has arrived in Qatar for a one-day trip to the small Gulf country as it faces a boycott by some of its Arab neighbours.