Zuckerberg said in a Facebook post that the Muslim community should not face discrimination following attacks in Paris and elsewhere linked to extremists.
His comments appeared aimed at countering the call by Republican presidential candidate Donald Trump to ban Muslims from entering the United States.
"After the Paris attacks and hate this week, I can only imagine the fear Muslims feel that they will be persecuted for the actions of others," he wrote.
"As a Jew, my parents taught me that we must stand up against attacks on all communities. Even if an attack isn't against you today, in time attacks on freedom for anyone will hurt everyone."
Trump caused international outrage Monday, when he demanded a ban on Muslims traveling to the United States.
He currently leads Republican polls by double digit margins over his nearest rivals. Fellow GOP candidates were among those condemning his plan, but senior party figures have refused to throw Trump under the bus, or even rule out voting for him.
"If you're a Muslim in this community, as the leader of Facebook I want you to know that you are always welcome here and that we will fight to protect your rights and create a peaceful and safe environment for you," Zuckerberg wrote.
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