Dr Ivan Patterson told his Church's annual assembly in Belfast that Christians may encounter challenges for living out their faith.
"Jesus speaks about going extra miles; welcoming strangers; loving enemies; forgiving those who do us harm," he said.
"In our society Christians have had their wings clipped in our politically correct world.
"It would seem that any philosophy is tolerated except that centred on Jesus Christ."
He pointed to the example of Christian doctor Richard Scott, who is being investigated by the General Medical Council after suggesting to a patient that he consider turning to Jesus as part of the healing process.
"Now he may have to pay the consequences of which he says he is willing to do and so may we if we are to be faithful to the Lord's commission," said Dr Patterson.
Dr Patterson, 62, was installed as Moderator during the opening session of the weeklong General Assembly, which is being attended by 1,200 Church members.
Calling for "sacrificial servants", Dr Patterson urged Christians to be distinctive whilst demonstrating love and tolerance towards people who are different.
"For an intolerant spirit defeats the Gospel," he said.
Dr Patterson has served as minister in Newcastle Presbyterian Church, Co Down, for the last 20 years.