A man who claimed he was suffering from sexsomnia when he had sex with a sleeping woman has been found not guilty of rape.

Trent John Pobar, 29, pleaded not guilty to raping his friend's partner in the Northern Territory town of Katherine in January last year.

Prior to the jury handing down its verdict in the Northern Territory Supreme Court, Justice Dean Mildren made a summary of the case for the jury.

The court heard Pobar had been drinking at the friend's house when he went into a bedroom and had sex with the woman.

She woke up and pushed him off, but Pobar said he had no memory of the incident.

The defence put the case that the accused had a history of parasomnia, which involves abnormal behaviour while asleep.

It said the incident in Katherine had all the indicators of sexsomnia, a form of parasomnia.

The judge said the prosecution was not convinced of this history, and it was instead arguing it was a case of amnesia caused by the large amount of alcohol Pobar had consumed.

This afternoon, the jury came back with a verdict of not guilty.

It is the second time such a defence has been successful in the Northern Territory.

Another man was acquitted in 2008 after a similar incident.