Uriah Levy had to fight his way through layers of entrenched prejudice in the Navy. When he tried to institute much-needed reforms such as eliminating flogging he was consistently hauled up before six court martials where time and again the blatant biases of his accusers were exposed. Abraham Lincoln signed into a bill that Levy had crusaded for decades: the prohibition of flogging. When the Civil War broke out, Levy again offered his services to the nation. Lincoln, with a twinkle in his eye, appointed Levy to position the U.S. Navy Court Martials Board. Lincoln explained that Levy had had a lot of experience with that agency that could now be put to good use.

In 1861, Congress established the office of Chaplin in the Union Army, but required that anyone appointed to the position "must be a regular ordained minister of some Christian denomination." On December 11, 1861, Abraham Lincoln received Rabbi Arnold Fischel of New York, who had been disqualified as Chaplin of "Cameron's Dragoon." Speaking for the Board of Delegates of American Israelites, the only nation-wide secular organization of Jews, Fischel presented a memorial that claimed that the chaplaincy acts "are oppressive in as much as they establish a prejudicial discrimination against a particular class of citizens on account of their religious beliefs" and violated the Constitution "in as much as they establish a religious test as a qualification for office under United States." Abraham Lincoln promised to help and in July 1863 Congress changed the offensive phrase to read "some religious denomination."

Six months after this affirmation of Jewish equality, came the single most blatant act of anti-Semitism that occurred in nineteenth-century America. When a Jewish community faced the threat of expulsion, Cesar Kaskel of Paducah Kentucky knew who could save Jewish people: Abraham Lincoln. During the Civil War, General Ulysses S. Grant issued his infamous General Order Number Eleven on December seventeen, eighteen sixty-two. He ordered Jews in Kentucky and Tennessee to be expelled from his command area within twenty-four hours as traitors to the Union. He declared the Jews were trading with the Confederate enemy. Grant would not listen to own father-in-law who was on friendly terms with Jews. All Jews not leaving would be arrested. In a few towns around Grant's headquarters at Holly Springs, Mississippi the order was actually carried out. Grant preferred not to discuss this incident in his Personal Memoirs. It was just too plain embarrassing. His order remains inexplicable to this day. Grant in dealing with Jewish officers and later as president never displayed the slightest sign of anti-Jewish prejudice.

Cesar Kaskel of Paducah, Kentucky sent a telegram and went to Washington plead his people's cause. On January three, eighteen sixty-three, he secured an audience with Abraham Lincoln. The president promptly ordered Army Chief of Staff Henry W. Halleck to countermand the order to help the "children of Israel." Halleck privately wrote Grant that Lincoln had "no objections to expelling traitors and Jew peddlers, which I suppose, was the object of your order; but as in terms proscribing an entire religious class, some of whom are fighting in our ranks, the President deemed it necessary to revoke it." Thus, Kaskel showed the Jews had to be proactive in helping to rescue themselves from persecution.

The New York Times reported on January 18, 1863 criticized the Jews delegation for being too "sycophantic." The order to be sure, was promptly set aside by President but the affront to the Jews conveyed by its issue was not so easily defeated. A committee of Jews took it upon themselves to thank President Lincoln at Washington for so promptly annulling the odious order. Against the conduct of the committee the bulk of the Jews vehemently protest. They say have no thanks for an act of simple and imperative justice, but grounds for deep and just complaint against the government, that General grant has not been dismissed from service.

One of Abraham Lincoln's campaign managers in the State of Illinois was Abraham Jonas. Jonas was an immigrant from England. In the area of frontier Illinois he settled, people came form miles around to see if had horns. His neighbor must have liked him because they elected him to the Illinois State Assembly where he met Abraham Lincoln and they became friends. Lincoln appointed Jonas to be the postmaster of Quincy, Illinois. All four of Jonas' sons fought for the confederacy. Lincoln released one son from a Union war prison camp to see his dying father. Lincoln appointed the widow to become postmistress Quincy,Illinois.

After Lincoln’s assassination, the Jews joined the rest of the nation in mourning. The Abraham and Straus in downtown Brooklyn became the center of that city's mourning ceremonies because it had the only statue of Lincoln at time.