Nintendo has been ordered by the court to pay Kyoto-based Tomita Technologies, patent holder of glasses-free 3D tech, a fee of 1.82 per cent of the wholesale price of every 3DS sold.
With 35 million 3DS units sold to date, Nintendo's bill to Tomita already stands at around $105 million.
The tech-firm had originally pushed for a flat fee from Nintendo for each 3DS sold, but the court ruled this would be unfair.
"If, as Tomita suggests, the ongoing royalty rate were expressed as a flat dollar amount per unit sold, Tomita would capture an increasingly large proportion of each sale as the price falls, even as the technology's reliance on the infringed patent remains constant," Judge Rakoff explained in a statement.
"This would result in an unearned windfall for Tomita, and, accordingly, the court prefers an ongoing royalty rate expressed as a percentage of wholesale price."