The campaign - launched in the wake of a Manhattan bomb attack blamed on a radicalized Afghan-American -initially will use social media to spread the message under the hashtag #IAmMuslimNYC.
"Now more than ever, it is important for every New Yorker to stand united as one city and reject hate and violence," said Mayor Bill de Blasio in a statement.
"We will not tolerate discrimination or violence of any kind and we will not rest until all New Yorkers, including our Muslim brothers and sisters, are treated with the dignity they deserve."
The campaign begins Tuesday, just 10 days after bombing suspect Ahmad Khan Rahami exploded a device in Chelsea, a fashionable Manhattan neighborhood, injuring 29 people.
Investigators say a handwritten manual recovered after his arrest lauded Al-Qaeda leaders including Osama bin Laden, and criticized US wars in Iraq, Afghanistan and Syria.
New York's campaign comes amid growing fears among the country's Muslims of a backlash over jihadist attacks, both in the United States and abroad, in the context of the anti-Muslim rhetoric embraced by Republican presidential hopeful Donald Trump.
Among the recent acts violence against Muslims in New York was the August fatal shooting of an imam and his assistant, execution-style, near their mosque in the borough of Queens.
New York is planning workshops beginning next month to give city employees and public and private employers a better understanding of Islam.
A marketing campaign using all media is in the works for around mid-2017 - when de Blasio's reelection campaign should be in full swing.
Since his first campaign in 2013, the New York mayor has promoted a multiracial and inclusive approach.
Before his election, he promised two school days off for Muslim holidays, on a par with Christian and Jewish holidays. That pledge has been in force since the start of the school year in 2015.
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