In 1892, Palmer accepted an offer by the president of the new "University of Chicago as non-resident dean of the women's department or the colleges and graduate schools. Her husband had also been offered a position, but he decided to stay at Cambridge.
She was required to be on-site for one third of the academic year. The goal of her office was to help students plan their educational career and create a social relationship between the university and its students. During her time as dean of the women's department she doubled the percentage of the female students at the school from 24% to 48%, which resulted in a backlash from mainly male faculty members. Discouraged by the faculty and staff's response, she resigned in 1895.
She had a number of suitors while at the University of Michigan and as she began her career, but waited to pursue marriage until she was established in her career with a comfortable income. Palmer had also been seen as the epitome of the "New Woman, and so some people were content that she remained an independent unmarried woman. During her time at Wellesley she met her future husband, "George Herbert Palmer, who taught at "Harvard University. She was engaged to marry George and resigned from her position at "Wellesley College in June 1887 partly due to her poor health. She had early signs of tuberculosis and was exhausted. Her new husband also felt that she had already made major strides towards improving the university. She took a break to recuperate.
Alice and George married on December 23, 1887 and she began to give public speeches on women's higher public education. They had a "marriage of comradeship". They both pursued their individual careers, and George contributed efforts to managing the household, particularly when she was at the University of Illinois during her post there.
While summering at her husband's home in "Boxford, Massachusetts, she explored the local area, sewed, watched birds, and took up photography. They took long trips to Europe over three of George's sabbaticals, during which they lived in their favorite cities and traveled through the countryside on bicycles. She composed many beautiful poems, some of which are found in Life of Alice Freeman Palmer and A Marriage Cycle. In 1901, she wrote the hymn How sweet and silent is the place (Holy Communion).
In December 1902, while the Palmers were in "Paris on sabbatical, she complained of pains that required surgery to remove a bowel obstruction.
During convalescence following surgery, she died of a heart attack. Palmer's life was commemorated at a service at "Harvard University in 1903 attended by college presidents whom she knew and other notable individuals in higher education.
George Herbert Palmer retained her ashes until 1909, when a monument was erected by sculptor "Daniel Chester French at Houghton Chapel in Wellesley College. At his request, George's ashes were entombed beside his wife's in 1933.
The Alice Freeman Palmer Institute, commonly called the "Palmer Memorial Institute, was founded in "Sedalia, North Carolina in 1902 for African-American students by "Charlotte Hawkins Brown, who was sponsored for her education and mentored by Palmer. Brown saw Palmer shortly before her death when she was fundraising for the school. It was named for Palmer following her death in December. In 1922, the school built the Alice Freeman Building, which held an auditorium, library, classes, and offices. It also had a collection of reproductions of art masterpieces, the first known school in the South for African-Americans to do so. In 1971, it was destroyed in a fire.
In 1908, the first endowment at the AAUW was created in Palmer's memory to help women attend colleges, conduct research, and write dissertations.
In 1920, Alice Freeman Palmer was elected to the "Hall of Fame for Great Americans.
In 1921, "Whittier College named a new women's literary society after her. The College had as its mission to create a female literary society, with the hope of bringing such groups back to Whittier College after they faded from existence at the beginning of World War I. Fullerton Junior College transfer "Jessamynn West and friends reportedly researched and lobbied extensively to name the group for Alice Freeman Palmer, due to her reputation as a staunch advocate of higher education for women during the late 19th century. In the early years, the Palmer Society was an intercollegiate society that read and performed plays with the school's cross-town rival, "Occidental College. Today, the Palmer Society's goal is still to "attain to the highest ideals of American womanhood."
In World War II, the United States "liberty ship SS Alice F. Palmer was named in her honor.