The often-foul mouthed Duterte made the joke in a speech to Filipino diplomats in his southern home town of Davao as he defended his bloody war on crime which has left thousands dead since he took office last year.
"What I don't like are kids (being raped.) You can mess with, maybe Miss Universe. Maybe I will even congratulate you for having the balls to rape somebody when you know you are going to die," for your crime, he said, implying the rapist would be lynched.
It was the latest in a series of off-colour jokes by Duterte who openly boasts of having mistresses and often makes sexual remarks about women.
Speaking in his rambling style, the president also boasted to the diplomats that he faked tuberculosis to escape mandatory military training in college.
But he also reiterated his vow to continue his bloody war on drugs despite accusations that thousands of suspects had been killed by police and vigilantes since he took office.
"Human rights? That is bullshit to me," he said, recalling how he called then-US president Barack Obama "a son of a whore" after Washington criticised the wave of killings.
Police say at least 3,200 people were slain in their anti-drug operations but rights groups charge that thousands more have been killed by vigilante groups.