Le Pen, 53, failed to unseat President Emmanuel Macron last weekend but achieved an historic score of 41.5 percent.
Erdogan, who in the past has traded barbs with Macron, hailed the election result.
“To put it correctly, the elimination and defeat of extremist ends in French elections is, in my opinion, a win because whatever we suffer is because of extremism,” Erdogan was quoted as saying by Hurriyet daily and several other media outlets, in comments to journalists on his plane back from Saudi Arabia.
Erdogan said he had hoped Macron would win and praised the French president for leading a “very smart” election strategy, especially during the debate.
“God willing, with the result of this election, our relations will be in a much better position,” he added.
Over the last few years, Turkey has been embroiled in a series of disputes with France and its EU partners, from tensions in the eastern Mediterranean to the contested Nagorno-Karabakh region.
The row escalated in 2020 when France moved to crack down on Islamist extremism after several attacks on its soil.
Erdogan, a pious Muslim, described Macron at the time as “trouble for France” and said he hoped that France would “get rid” of Macron “as soon as possible”.