News agency AFP reported that more than 50 refugees arrived in Champagne-sur-Seine in north-central France, about an hour from Paris. More were welcomed in the department of Yvelines.
In total, 200 are expected to arrive in France on Wednesday and the Red Cross expects about a thousand refugees arriving from Germany by Friday.
French President Francois Hollande announced Monday that France will take in 24,000 refugees over the next two years and launch surveillance flights over Islamic State armed group positions in Syria.
"Now is not the time to take fright, it is time for bold, determined action for the European Union," Juncker said to applause from the European Parliament in Strasbourg in his first State of the Union speech.
"There are 160,000 people that Europe must take into its arms, and this has to be done in a compulsory way. I call on the (European) Council to agree to take 160,000 at the interior ministers' meeting on September 14," he said.
But he warned EU member states against making religious distinctions when deciding to admit refugees as he recalled Europe's past of religious persecution.
"There is no religion, there is no belief, there is no philosophy when it comes to refugees," Juncker said. "We don't distinguish."
The French government on Tuesday condemned two mayors who said they would only take in Christian refugees.
Meanwhile, Hungry's Prime Minister Viktor Orban warned last week that the wave of mostly Muslim refugees coming to Europe threatens to undermine the continent's Christian roots an idea rejected by German Chancellor Angela Merkel.
Merkel on Wednesday urged Europe to go further, claiming binding quotas were the only way to ensure a "fair" and proportionate sharing of the burden.
Germany expects 800,000 asylum claims this year and has said it could take half a million annually over several years.
Mandatory quotas have faced stiff opposition, especially from eastern EU states such as Hungary, which is on the front line of Europe's largest migrant wave in 70 years.