Suffolk County officials arrested Brendan Sullivan on Thursday in a parking lot on Medford Avenue in Patchogue around 3 p.m.
They say Sullivan had sexual contact with two 13-year-old girls on separate occasions in March and August.
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According to police, he used Snapchat to meet his victims.
Sullivan was arrested in May on charges related to child pornography.
A follow-up investigation of that case made by detectives revealed Sullivan had inappropriate contact with the two female victims.
Sullivan was charged with two counts of second-degree rape and three counts of child endangerment.
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He is being held overnight and is scheduled to be arraigned in court on Friday.
The investigation is ongoing.
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