Emanuel, who was in New York for a series of meetings, entered Trump Tower just after 9 a.m. central time to meet with the president-elect. He left approximately 75 minutes later.
A Trump spokesman would not say why Trump decided to meet with Emanuel but that the president-elect has met "taken a broad range of meetings so far" with "people who have good ideas and advice on tackling particular issues."
The mayor gave Trump a letter signed by 14 mayors from across the country urging the president-elect to continue the program started by President Barack Obama that gave legal status to immigrants who came to America as children known as "dreamers."
The program should be continued until Congress modernizes the immigration system and provides a more permanent form of relief for those immigrants, according to the letter.
As he was leaving Trump Tower, Emanuel told the news media that the nearly one million "dreamers" who were brought here by their parents before they turned 16 were "working hard toward the American dream" by going to school and joining the U.S. Military.
"They are something we should hold up and embrace," Emanuel said, calling his session with Trump "a good meeting."
Eliminating the Deferred Action for Childhood Arrivals program would "lead to the loss of $9.9 billion in tax contributions over the next four years and would wipe out at least $433.4 billion from the U.S. gross domestic product during the next decade," according to the letter.
Emanuel said he also "spoke out strongly" about his commitment to Chicago remaining a sanctuary city that "will support and secure the people who are here."
Trump has promised to withhold federal funds from municipalities that protect undocumented immigrants from deportation, sources said.
Trump made immigration a central issue of the presidential campaign. He has vowed to build a wall between the United States and Mexico, to deport 11 million undocumented immigrants and to ban Muslims from entering the country.
The mayor said he and the president elect also discussed Chicago's transportation infrastructure, which Emanuel has been working to modernize in an effort to boost the area's economy.
City officials are waiting to hear whether their effort to secure $1.1 billion in federal money for the renovation of the Red and Purple CTA train lines before Obama leaves office. After Trump takes, city officials are expected to ask for another billion dollars to fund the extension of the Red Line south to 130th Street.
In addition, Emanuel said he touted the rising graduation rate at city schools, as well as his push to offer courses at the seven City Colleges of Chicago that prepare students for jobs in high-demand fields during his meeting with Trump.
Emanuel also touted the Chicago Star Scholarship program in his meeting with the president-elect. That program gives Chicago Public Schools students graduating with at least a 3.0 grade-point average free rides to the seven City Colleges.
Those scholarships — which Emanuel has touted as a "ticket to the middle class" — are available to students regardless of their immigration status, officials said.
"Through transportation, talent, and training, [we] can drive economic growth," Emanuel said.
The President-elect asked for the meeting with Emanuel, "as he has done with others who have significant experience in the White House and several other big city mayors," mayoral spokesman Adam Collins said in a statement.
Emanuel, who served as Obama's first chief of staff and as an aide to President Bill Clinton, said he offered the president-elect and his Chief of Staff Reince Priebus and Chief Strategist Steve Bannon insights from his time in the White House — "how to make that work."
Emanuel — although he stayed on the sidelines for much of the presidential election — criticized Trump as unfit to lead America during the campaign.
Since Trump's election, Emanuel has made a series of announcements designed to reassure immigrants in Chicago that he will take steps to protect them from a Trump administration.
A new 23-member task force announced Tuesday with U.S. Sen. Richard Durbin and U.S. Rep. Luis Gutierrez, will "collaborate on mental health, legal services, diversity training for employers and education" to make certain the city is delivering "comprehensive services to immigrants, refugees and other disenfranchised communities," officials said.
The "Chicago Is With You" task force will develop a website that will serve as a source of information for immigrants and connect undocumented immigrants with those who have volunteered to help them.
Emanuel has said he was not worried about Trump taking revenge on Chicago officials, who voted to remove a street sign honoring him outside Trump Tower and blasted him as a racist who should not be allowed to occupy the White House.
During the campaign, Trump held up Chicago as the embodiment of all that is wrong with urban America — a "war-torn country" rife with voter fraud and consumed with violence and poverty.
Read the full letter Emanuel delivered to Trump here:
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