The separation from Coyote Shivers was tumultuous, marked by allegations from Perrette of compulsive lying, lack of trust, stalking, and posing as a woman online to approach her. Pauley even obtained a restraining order against him, expressing fear for her safety in a 2018 interview with 48 Hours.
Following her divorce, Perrette was engaged twice but did not proceed to marriage in either case. She was engaged to cameraman Michael Bosman, with whom she exchanged vows in a commitment ceremony but decided not to legally wed until same-sex marriage became legal in California. They eventually parted ways in 2008. Later, she got engaged to former British Royal Marine Thomas Arklie in 2011, but the relationship ended in 2019.
As of 2019, Pauley Perrette announced her single status on Twitter, stating that she had chosen to be celibate and emphasizing her independent stance. She humorously shared an encounter with a fireman resembling her “imaginary firefighter boyfriend” but clarified her commitment to a solo life.