The evangelist praised from Tastries Baker in Bakersfield, California for standing up for her beliefs, despite the prospect her business could be forced to shut.
While a judge refused a bid by the state government earlier this month to force the firm's closure unless it reversed its stance, the case continues - with another hearing due for February 2018.
Franklin Graham wrote on his Facebook page: "I appreciate the fact that Cathy Miller stood up for her beliefs...
"We need to pray for Cathy and for our religious freedoms to be upheld.
"The courts should never be able to force Christians to go against what the Word of God teaches."
The 65-year-old accused members of the lesbian, gay, bisexual and transgender community of trying to force believers to embrace their lifestyles.
He went on to say: "It ain't gonna happen.
"God calls homosexuality sin - take it up with Him if you don't like it."
"As a Christian of course I don't hate gays, I love them and want them to know the truth.
"If they choose to live that lifestyle, they certainly have the freedom to do so in this country-but don't tell me what I have to believe or participate in."
Franklin Graham's new remarks are likely to add strength to calls among LGBT advocates that he ought to be prevented from attending a rally in Blackpool next year.
A number of Lancashire MPs have expressed concern over the visit, while more than 7,000 people have signed a petition calling upon the Government to refuse him entry to the UK.