His decision put his fate back into the hands of the church that put him on trial for officiating at the same-sex wedding of his son Tim in 2007 in Massachusetts. And it continued to hold the spotlight on the United Methodist Church as it and other denominations grapple with the legal and moral issues of gay marriage.
Schaefer is among a half-dozen clergy to be put on trial by the United Methodist Church since 1999. At least three more trials are looming for ministers around the country who officiated at same-sex weddings or are openly gay, advocates say.
On Monday, more than 50 supporters - many fellow ministers - attended the announcement. As Schaefer stood in front of an altar decorated with holiday garland and a glittering tree and said he would not quit, the group erupted in applause.
One man, who declined to give his name, shouted that he was prepared to give up his own credentials if Schaefer loses his when he meets with church leaders Thursday.
Schaefer said the public response to decisions he has reached in prayer has surprised him. He was unsure whether this decision, which he said he knows seems rebellious, would be supported.
"I can't go back to saying, 'Yeah, well, that law is in place and I broke it, but I broke it for a good reason,' " Schaefer said after the news conference. "I'm past that. I've gone on record - and not just on record, but in my heart of hearts - I've said I will call [the church policy] by what it is."
And that, he said, is discriminatory.
Schaefer has been suspended from his post at Zion United Methodist Church of Iona since his Nov. 19 sentencing.
At the end of that two-day trial, in the gymnasium of a Methodist retreat center in Spring City, Chester County, the jury told Schaefer he had 30 days to recommit himself to the church's laws or leave the ministry.
On Thursday, he will meet with a board of pastors at the Norristown office of the church's Eastern Pennsylvania Conference. Schaefer said that group could defrock him or let him continue to minister - effectively letting him stand as a voice for marriage equality within a church deeply divided over the issue.
Advocates for social change within the church, which has about 12 million members worldwide, have said three other Methodist ministers in the United States are awaiting trials and at least three others have had complaints, but not charges, filed against them.
Several at Monday's news conference also took part in a ceremony at the Arch Street church last month in which about 50 pastors jointly blessed a same-sex wedding. Bishop Peggy Johnson, who oversees the conference, has not said whether those ministers will be disciplined.
Schaefer and more than 40 other pastors gave Johnson a petition calling for her to refrain from holding trials, acknowledge that some church laws are discriminatory, and call for a process of prayer and change.
Johnson declined an interview request Monday. In a statement, she said that the Methodist book of discipline "is not a perfect document." She pointed out parts of it that affirm homosexual church members.
She said some within the church would like to see more trials because Schaefer's garnered such a strong public outcry against the church's position.
Schaefer said many supporters encouraged him to say he could uphold the church's laws, then live by his own interpretation of those rules.
But the pastor, who has three gay children, said that would have been disingenuous in light of his statement on the second day of his trial, when he slipped a rainbow stole over his shoulders and said he would continue to advocate for gay rights.
Prior to that moment - which came after he had been convicted but before he had been sentenced - Schaefer's defense team had tried to convince the jury that his actions broke some church rules but upheld others, including a directive to minister to all people.
Schaefer said he wants to continue ministering within the United Methodist Church but believes there is a good chance he will be defrocked. He said he has been approached by other denominations, including the United Church of Christ and the Episcopal Church, about ministering with them. But he said he would not consider those options unless his credentials were taken from him.
He said he could not give them up on his own because they were given not just by the church, but by God.
"I don't take this lightly," he said. "It's not like a job contract that is between the company and its employee. This is a far greater thing."