The 15-year-old boy was arrested shortly after the man, named only as Harry H., was found stabbed to death outside his flat in the Spandau district of Berlin on Thursday afternoon. Initial reports suggest he was stabbed at least three times.
Investigators say the two knew each other, and that their work was focussing on whether the teenager had been sexually abused by the man.
The boy has reportedly admitted killing the man, and is being held in youth detention.
The dead man had two convictions for sex offences against children over the past 10 years. One case resulted in a prison sentence of more than three years, the Tagesspiegel newspaper reported.
The BZ newspaper said Harry H. had not made any secret of his liking of young boys, and had invited several local youths to his flat where they were allowed to play computer video games and watch pornography.