Sirisena, who met relatives of the teenager killed in the in the country's north about two weeks ago, said he would ensure justice to the victim's family.
His unannounced visit to Jaffna came as police obtained a new court order banning protests for two more weeks.
The gangrape and murder of the girl has fuelled tensions in the former warzone and sparked clashes between residents and police, who have been accused of failing to act swiftly.
Police have also come under mob attacks and a local court building was damaged by enraged residents last week, after the victim's body was found in Punguduthivu area on May 14.
The bruised body was found a day after the girl had gone missing.
About 130 people, who allegedly took part in the protests following the recovery of the body, have been arrested.
The police have also fired tear gas on the protesters in the days after the body was recovered, fuelling more anger.
Sirisena, who came to power in January, said legal action would be taken against those who pelted stones at Jaffna Police and the court.
In Jaffna, the former epicentre of the decades-long separatist conflict between the LTTE and the Sri Lankan army, the protests were a rare public outbursts since the end of the war that left at least 100,000 people dead.
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