But Davis' lawyer told U.S. District Judge David Bunning that his client would not allow her deputies to issue the licenses. Davis was not in the courtroom for the second session. She was in a hallway outside.
"We cannot represent to the court that she would allow licenses to be issued," attorney Mat Staver said.
Staver later told CNN's "The Lead with Jake Tapper" that Davis would issue licenses if her name and title were not on them.
"Because that in her understanding and mind is authorizing something that is contrary to her Christian values and convictions," he said. "That's where the conscience rub is."
Earlier Thursday, Bunning remanded Davis into the custody of U.S. marshals for refusing to heed a U.S. Supreme Court order legalizing same-sex marriage, saying she would remain in jail until she complies with the ruling.
Bunning then asked Davis' six deputy clerks whether they would issue the licenses, and despite some of them holding the same religious beliefs as Davis, five told Bunning they would issue the licenses. The sixth -- Davis' son, Nathan -- didn't answer.
Gov. Steve Beshear said the judge's decision "speaks for itself."
"The future of the Rowan County Clerk continues to be a matter between her and the courts. Deputy clerks have said they will commence issuing marriage licenses beginning (Friday)," he said. "It appears that the citizens of Rowan County will now have access to all the services from the clerk's office to which they are entitled."
The governor said he had no authority to use an executive order to relieve a county clerk of his or her duty.
During Davis' hearing, April Miller told the court that the clerk had denied her a marriage license three times, and when Davis took the stand to deliver her at-times emotional testimony, she explained that she could not issue the licenses because of her religious beliefs.
"You can't be separated from something that's in your heart and in your soul," she told the judge, according to CNN affiliate WKYT-TV
American Civil liberties Union attorneys argued in a motion filed Monday
that Davis "continues to collect compensation from the Commonwealth for duties she fails to perform."
They said they didn't want her to be jailed as punishment, but rather, the attorneys asked the court to "impose financial penalties sufficiently serious and increasingly onerous" to make her comply with the court order.
Bunning, however, apparently felt she deserved jail time, but he also told Davis she could end her incarceration by complying with the Supreme Court order and telling her deputy clerks to do the same.
He said he didn't believe fining Davis would convince her to comply with the high court ruling, especially considering that Davis had testified earlier that her supporters are raising funds for her and calling her office to offer financial support, WKYT reported.
'She can't disobey her conscience'
Bunning said he, too, was religious, but he explained that when he took his oath to become a judge, that oath trumped his personal beliefs, the station reported.
"Her good faith belief is simply not a viable defense," Bunning said.
Davis thanked the judge for his ruling, according to WKYT. She was not placed in handcuffs, but a U.S. marshal led her out of the courtroom.
Celebrations and protests erupted outside the courthouse in Ashland when those who attended the hearing exited the courtroom with news of the decision. Chants of "Love won! Love won!" filled the air.
Staver, founder of Liberty Counsel, which represented Davis, said he was "stunned" by the judge's ruling.
"Knowing Kim Davis and her strong Christian resolve and convictions, she may be jailed behind bars, but her conscience remains free," he told CNN.
He said his client had became a different person 4 1/2 years ago after attending a church service that affected her beliefs.
"That is the reason why her conscience is so strong," he said. "She loves her Lord, she loves God, and she can't disobey her conscience or be disobedient."
Davis, an Apostolic Christian
who says she has a sincere religious objection to same-sex marriage, has refused to issue any marriage licenses since the Supreme Court decision in June legalizing same-sex marriage
In court documents filed Wednesday
, her attorneys argue that she shouldn't be held in contempt. Instead, they argued, there are alternatives that would allow couples to get marriage licenses in Rowan County without going against Davis' religious beliefs.
Among the options they offered were allowing other officials to issue marriage licenses in the county, distributing marriage licenses at the state level or changing marriage license forms to remove Davis' name.
A seat inside the courtroom was a hot ticket. Before the session began, more than 100 people were turned away from Bunning's courtroom, which holds 300 people. A federal law enforcement source told CNN that because of the controversy surrounding the case, Bunning was provided with a security escort on his way into work.
'Respect the law; do your job!'
A large crowd, leaning mostly in support of Davis, gathered outside the courthouse before the hearing, many carrying signs. "Jesus Saves" read one, "Homo sex is sin," read another, while one sign pointed passers-by to the Bible's Acts 5:29, which quotes Peter and other apostles saying, "We must obey God rather than human beings!"
Lana Bailey of Worthington, about a 20-minute drive northwest of Ashland, brought signs as well, both of which seemed to address Davis: "My gay friends pay taxes which helps pay you... right??" and "Respect the law; do your job!"
"I'm here to support equal rights for all," she said. "It's just called respect. I don't understand why we're having this. Why are we spending money on this? ... If you can't do your job then you need to step down. You need to resign."
Jason Porter, a pastor at Ashland's Gospel Light Baptist Church, spoke for the other side and said he wasn't at the courthouse "to bash people's decisions and lifestyles," but he worried that if people were allowed to continue doing whatever they want to do, "the floodgates will open to other areas of polygamy."
He did not elaborate on how same-sex marriage was akin to polygamy, which is the act of having multiple spouses. Polygamy is illegal in every state.
Echoing those who cited Acts 5:29, he said he felt Davis had a right to refuse to issue the marriage license and, waving his Bible, he told CNN he bore no hatred toward gay couples and is merely standing "for the truths of my God's word."
"I just know the destruction that this brings. As a pastor, I see the background. I see the broken families. I see the AIDS. I see the folks dying of diseases and the brokenness of relationships," he said.
Lawyers: Issuing licenses 'violates her conscience'
Two other county clerks in Kentucky are also refusing to issue same-sex marriage licenses, according to a statement on Beshear's website.
Bunning ordered Davis to resume the issuing of marriage licenses on August 12. Monday night, the Supreme Court denied an emergency application from Davis, who asked that Bunning's order be put on hold pending appeal.
In a statement released Tuesday, Davis, a Democrat, said she has received death threats but intends to continue to serve as the county clerk -- a position she was elected to fill in November.
In court papers, attorneys for Davis argued that she is unable to comply with the court orders because issuing same-sex marriage licenses "irreparably and irreversibly violates her conscience."
Finding her in contempt of court, they argued in the motion filed Wednesday, also would "substantially burden Davis' religious exercise."
But some scoff at the clerk, suggesting she's a hypocrite because she's been divorced three times
Davis said she's a different person now since becoming a Christian four years ago.
"I am not perfect," she said in a statement. "No one is. But I am forgiven."
The ACLU attorneys, who represent two same-sex couples and two opposite-sex couples who want to get married in Rowan County, argued that Davis has no legal basis to avoid performing her duties as a government clerk.
And a federal prosecutor said it's time for Davis and her county to comply.
"Government officials are free to disagree with the law, but not disobey it," U.S. Attorney Kerry B. Harvey said in a statement. "The County Clerk has presented her position through the federal court system, all of the way to the U.S. Supreme Court. It is time for the Clerk and the County to follow the law."