John J. DeGioia, president of the Catholic university, sent an email to students Wednesday night saying, "We have been confronted with an abhorrent act of anti-Semitism."
He said the symbol was "accompanied by threatening and derogatory language advocating for violence against women."
D.C. and campus police are investigating it as a hate crime.
DeGioia said in the email, provided by a university spokeswoman, Wednesday's incident at LXR residence hall was the third time a swastika was found in a student apartment building in recent weeks, and the second time at LXR. The hall was once three separate buildings with names Loyola, Xavier and Ryder.
Officials provided no details about who found the swastika, which was painted inside a women's bathroom stall, but said it was discovered the same night the university held Rosh Hashanah — or Jewish New Year — services at Gaston Hall, an auditorium at the student life center about three blocks from LXR residence hall.
"There is never a time or place for these acts, and this incident is even more disturbing during Rosh Hashanah," DeGioia said in his email. "We stand in solidarity with our Jewish community and strongly condemn this act of hate, anti-Semitism, and sexism."
The university president vowed "those found responsible for these acts of hate will be held fully accountable for their actions."
He also noted efforts to prevent such bias incidents from occurring, citing several initiatives to reach out to communities of different faiths and backgrounds.
"Ours is a community where all faiths are welcomed, and where we choose to come together in understanding and service towards one another," DeGioia said in the email.