Barnardo's Cymru said professionals can often spot symptoms of abuse among girls, but sexual stereotyping means boys can slip through the net.
Negative behaviour among boys tends to be taken at face value, while in girls it is more likely to be explored as a potential response to trauma.
The charity wants awareness raised.
Menna Thomas, senior policy research officer and co-author of the report, I Never Spoke About It, said boys have "additional barriers which prevent them from being identified and, more importantly, from being able to speak up about their abuse.
"For example, boys' negative or criminal behaviour is often interpreted and responded to in a way which overlooks their status as victims of exploitation and abuse.
"There doesn't seem to be sufficient awareness of the possibility of boys being vulnerable to sexual exploitation and, therefore, insufficient messaging to boys that they will be believed and offered suitable services."
The report also found as the most vulnerable boys move into adolescence, they are at greater risk of mental health problems, substance misuse, homelessness and offending behaviour.
It found they were also more likely to be loners - all are factors which can increase the risk of sexual exploitation.
It said a high number of professionals who were questioned referred to boys who had run away from home or been forced to live on the streets and exchanged sex for accommodation or food, known as "survival sex".
Boy victims of sexual exploitation often miss out on help as they are more reluctant than girls to admit their abuse, a charity has warned.