The 1999–2000 ISU Junior Grand Prix was the third season of the ISU Junior Grand Prix, a series of international junior level competitions organized by the International Skating Union. It was the junior-level complement to the Grand Prix of Figure Skating, which was for senior-level skaters. Skaters competed in the disciplines of men's singles, ladies' singles, pair skating, and ice dance. The top skaters from the series met at the Junior Grand Prix Final.