Revd Susan Boyce was giving evidence at the Old Bailey, in the trial of four others accused of terrorism charges.
The four deny the charges against them.
Mrs Boyce told the Old Bailey her son Jacob Petty converted to Islam aged 15, and told his parents he was joining Islamic State in August 2015.
The minister said: "He rang at the end of August to say he was going to Syria.
"I was horrified.
"I just expressed 'do not be so stupid, don't do it, don't go there'.
"I had no idea Jake had thoughts of going to Syria. There were Sunni Muslims involved in Islamic State but he was quite horrified by what he saw watching it on TV."
After regularly contacting each other while Jacob was in Syria, the two lost contact in December 2014.
It was at this point that he is thought to have been killed, aged 25.
Police confirmed this in October 2015 by showing Revd Boyce footage of son's dead body.
The trial of the four defendants continues.
