The pregnant wife of the pastor of Resonate Church in Indianapolis has died after being shot in the head at her home by intruders, according to church officials.

Her husband, Davey Blackburn, has said that "as deeply as I am hurting, I am hopeful and confident that good things will come of this."

Amanda Grace Blackburn, who was 12 weeks pregnant according to family and friends, died in hospital on Wednesday morning after she was shot in the head at her home.

A Facebook post from the church just after 11:30 on Wednesday said: "Extremely heavy hearts today. Our pastor's wife, Amanda Blackburn, passed away this morning. Please pray for the Blackburn and Byars family during this difficult time. Although we are hurting tremendously, we are still hoping and believing that great things are still yet to come from this. 'Although we don't know what to do, our eyes are on you.'"

Blackburn's father-in-law had posted on Facebook earlier that there was a bullet lodged in her head and that doctors were testing her brain activity and blood flow.

WTHR reported that Blackburn, 28, was at home with Winston, her one-year-old toddler, who was not injured. Davey, who was reportedly at the gym and found his wife wounded when he returned at 8:30am.

"We found the adult female victim in the home unconscious [with] head trauma. She was transported to Methodist Hospital in critical condition," said offer Raphael Diaz.

Three hours before Blackburn was found, a nearby house was burgled. Police are yet clear as to whether the two incidents are connected.

Davey Blackburn was a youth pastor at NewSpring, Anderson before moving to Indianapolis to plant Resonate Church with his wife in January 2012.

He wrote a letter to his church yesterday which said, while "it's impossible to communicate all the emotions my heart has been forced to process" he remains "hopeful and confident that good things will come of this.

"I rest in the truth of Romans 8:28 that God works all things together for the good of those who love Him and who are called according to His purpose."

Inspired by his wife's "mission to see as many people as possible come to know Jesus as their personal saviour", he said "I know that in her death and legacy even more people will come to a saving faith in Christ.

"I hold firm to the belief that God is still good, that He takes our tragedy and turns it into triumph, and that the best is truly yet to come."