The young supporter is reported to have filed a complaint with police, alleging that the Borussia Dortmund striker struck him on the forehead as Lewandowski drove by his home in Dortmund.
Lewandowski, whose decision to join Dortmund's Bundesliga rivals Bayern Munich next season has angered many fans, is said to have stopped his vehicle and got out to confront the teenager.
However, the 25-year-old vehemently denies accusations of violence.
"I want to clearly state that I never used violence against people who violated my private sphere," Lewandowski said in a statement on his Facebook page.
"I have no intention of teaching teenagers how to behave but I will not allow for my family and myself to be offended."
Poland international Lewandowski, who has signed a five-year contract at the Allianz Arena from the 2014-15 season, has received the backing of his current club.
"Robert explained that the boy showed him the middle finger, he then got out of the car, put his hand on his shoulder and asked him why he was doing such a thing," Dortmund chief executive Hans-Joachim Watzke told Bild.
"Robert swears he never hit the boy in the face and that he never even touched him. I believe Robert 100 per cent."
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