Last year Dr Larycia Alaine Hawkins vowed to wear the hijab "in solidarity with our Muslims sisters" because she claimed it was her duty to love others.
Quoting Pope Francis, she asserted that Christians and Muslims "worship the same God" and are "formed of the same primordial clay".
But she was placed on leave by the evangelical Wheaton College and has since agreed to exit her role.
In a joint statement issued yesterday, Dr Hawkins said she had reached "place of resolution" with he college.
College president Dr Philip Graham Ryken thanked the professor for her "contributions to this institution over the last nine years".
He added: "We are grateful for her passionate teaching, scholarship, community service and mentorship of our students."
Dr Hawkins announced her decision to wear the headscarf in December, days after a Muslim couple carried out a terror attack in San Bernardino, California.
She said: "I don't love my Muslim neighbour because s/he is American. I love my Muslim neighbour because s/he deserves love by virtue of her/his human dignity."
She added: "I stand in religious solidarity with Muslims because they, like me, a Christian, are people of the book.
"And as Pope Francis stated last week, we worship the same God."
She was placed on paid administrative leave but nearly 80 staff members urged the Illinois college to reinstate her.
In response to the suspension, she said: "Wheaton College cannot scare me into walking away from the truth that all humans, Muslims, the vulnerable, the oppressed of any ilk, are all my sisters and brothers.
"And I am called by Jesus to walk with them in their oppression."
