The visit by the far right firebrand came a day after Russian Foreign Minister Sergei Lavrov hailed Ms Le Pen and US President Donald Trump as "realists" and not as representatives of "populist" political views.
"We attach a lot of importance to our relations with France, trying to maintain smooth relations with both the acting power and the opposition representatives", Putin said.
"A new world has emerged in the past years".
Ludovic de Danne, Ms Le Pen's global advisor who took part in the meeting with Mr Putin, said: "He wished her good luck".
There was no mention, either from Le Pen, or from the Kremlin, of the prospect of getting more money to finance her party's election campaign. "I know that you represent a European political force that is growing quickly".
Le Pen met with Russian lawmakers earlier in the day, including attending a meeting of the lower house of parliament's worldwide affairs committee upon an invitation by the committee's chairman Leonid Slutsky.
Fillon, who has been equally outspoken about the need for a rapprochement with Russia, has enjoyed extremely favorable coverage on Russian state TV. There is little doubt Russian Federation would be happy to deal with a President Le Pen.
Salute to Chuck Berry opens Rock Hall ceremony
To be eligible, all of the nominees had to have released their first recording no later than 1991. Inductees will eventually be enshrined in the Rock and Roll Hall of Fame museum in Cleveland.
Ms Le Pen favours strong links between France and Russian Federation, and wants the European Union to lift sanctions imposed on Moscow over the annexation of Crimea from Ukraine.
It is rare, however, for Putin to meet a foreign presidential candidate so close to an election. The European Parliament on March 2, 2017 lifted French far-right leader Marine Le Pen's immunity from prosecution over her tweeting of images of Islamic State atrocities.
Le Pen herself has repeatedly visited Russia, and her party borrowed 9 million euros in 2014 from the small First Czech Russian Bank, but the bank's license was later revoked.
Ms Le Pen, who is an admirer of Mr Putin, is polling to reach the run-off in France's presidential election on May 7 but to lose to independent centrist Emmanuel Macron.
USA authorities have accused the Russian government of using cyberattacks to meddle its presidential election past year.
"We reject the diplomacy of threats, the diplomacy of sanctions, the diplomacy of blackmail that the European Union has been using increasingly often, not only against Russian Federation, but also against its own members", TASS cited the French politician as saying.
Putin said Russian Federation has no intention of influencing domestic affairs in France but reserves the right to maintain contacts with representatives of all political forces in that country.