James McConnell made the comments while preaching at Whitewell Metropolitan Tabernacle church in Belfast.
After the sermon was posted online, a number of complaints were made, which led to an apology from Mr McConnell.
However after police questioning, the 78 year old is reported to have refused to accept a lesser punishment which meant the case would not have gone to court.
A spokesperson for the Northern Ireland's Public Prosecution Service said: "I can confirm that following consideration of a complaint in relation to an internet broadcast of a sermon in May 2014, a decision was taken to offer an individual an informed warning for an offence contrary to the Communications Act 2003.
"That offence was one of sending, or causing to be sent, by means of a public electronic communications network, a message or other matter that was grossly offensive. The offer of an informed warning was refused by the defendant and accordingly the matter is now proceeding by way of a summary prosecution in the Magistrates Court."
Shortly after the incident, Northern Ireland's First Minister Peter Robinson also had to apologise after appearing to defend the pastor.
He had said he would not trust Muslims for spiritual guidance but would trust them to "go down to the shops" for him.
It has not been revealed when Pastor McConnell's case will go to court.