The attack happened on Tuesday afternoon at a parking lot adjacent to a church in the Södermalm district of Stockholm.
The 24-year-old had come by the church on Monday to speak to the priest. He asked her if she had previously worked in Tumba, a southern Stockholm suburb, a source told the Aftonbladet newspaper.
The priest replied that she had not worked in Tumba. However, on Tuesday, the man returned and asked to see her again.
The priest thought the man seemed unpleasant and was afraid he would be waiting for her outside the church. She therefore asked a colleague to accompany her to her car after finishing work.
The priest and her colleague could not see the man and so she walked up to the car alone.
When she was about to unlock the car door, the 24-year-old appeared from behind and hit her in the head several times with a hammer
"I am going to kill you!" he is reported to have shouted.
The priest's colleague and several passers-by managed to overpower the attacker and contained him until police arrived to arrest him.
According to Aftonbladet, the 24-year-old allegedly had been looking up people from his childhood in Tumba and by chance found the female priest. However, she says she has not encountered him before.
The priest spent Tuesday night in hospital.
"She is of course affected by the events and does not feel well. Hopefully she has not suffered any permanent physical injuries," the priest's legal counsel told the paper.
On Friday, the 24-year-old was ordered remanded in custody. His trial is expected to commence on November 1st and the district court has determined that he should undergo a psychiatric examination.
He is previously known by the police but has never been charged for any serious crime.