Carson Smith, the sheriff of Pender county, told Deborah Hobbs, 40, that her decision to cohabit was a moral and a legal issue.
"This is sort of like a double barrel," he told Star-News Wilmington. "It is a violation of general statute, and it goes against something that I believe - it is a moral issue ... Personally and morally, I think it's best to be married if you're going to be living together."
North Carolina is one of seven states, including Mississippi, Florida, Michigan, Virginia, West Virginia and North Dakota, which prohibit cohabitation.
A 200-year-old law which outlaws fornication and adultery for "a man and a woman, not being married together", who live "lewdly and lasciviously" could result in a fine of $1,000 (£539) and up to 60 days in jail. Between 1997 and 2003 35 people were charged under it, of whom seven were convicted.
Ms Hobbs, who has been living with her partner for 12 years, filed a lawsuit in March to get the law changed.
"I don't want this to come off negative to Sheriff Smith," she said after she was fired. "He is a good person. I want my fight to be about this law."
The American Civil Liberties Union has taken up Ms Hobbs' case. North Carolina's law is considered vulnerable after the 2003 supreme court ruling on Texas's anti-sodomy laws, which made it more difficult for states to enforce laws regarding sexual behaviour.
"Certainly the government has no right regulating relationships between consenting adults in the privacy of their own homes," said Jennifer Rudinger, the executive director of North Carolina's ACLU.
"This law is 200 years old and a lot of people are very surprised that we even have it on the books."