The 24-year-old, whose name has not been divulged, is alleged to have raped the boy in the toilet of a private school in December last year, the Gulf Daily News reported Tuesday.
The accused has pleaded not guilty in a criminal court.
The boy, the son of a policeman, testified that he had left the toilet door open when the cleaner came from behind, grabbed him and raped him.
A medical test later confirmed rape.
The cleaner has claimed that male cleaners are not allowed inside the boys' toilet.
The court's ruling is expected June 11.