Joy Everingham, 46, who serves at St Peter's in Canterbury, spent decades secretly wearing women's clothes before telling her wife what she had been doing.
Everingham told Kent Online: "We were sitting in bed and I said 'I've got something to tell you'.
"I started crying and couldn't breathe. It was probably the hardest thing I've ever done.
"I thought she was going to leave me, or kick me out, but she said 'I've got to think about this'."
The minister said while her wife was prepared to help her explore her identity, she was "adamant that if I transitioned to a woman she wouldn't stick around'."
The couple donated all of Everingham's female clothes to charity in 2002 after the birth of their second son but not being able to live as a women sent her into a spiral of depression.
After being diagnosed with gender dysphoria, she explained: "Sometimes I felt like God had cursed me, but I had to trust in a god that loves me, whatever I am."
While training to become a minister, the couple decided to tell their sons and church that Everingham planned to transition, before becoming ordained last summer.
It is the first time a transgender person has been appointed as a minister in the church with the church's knowledge.
The parent-of-two from Canterbury, Kent, says she first knew she was different aged just five, and 'didn't fit in with everyone else'.
She told the Times: "I wasn't like the boys, I was always more like the girls."
She now lives as a woman full-time and 18 months ago started taking cross-sex hormones.
The minister said her wife "loves me for who I am, but she's still attracted to men".
She added: "I'm not sure she is really attracted to me sexually anymore, but we're still in love and we're still best friends."
