A novel soybean cultivar designated S52-U3 with high yield potential, tolerance to Roundup herbicide, early MG V maturity, and resistance to races 3, 9 and 14 of Soybean Cyst Nematode, further including the plants and seeds of the cultivar S52-U3, methods for producing a soybean plant by crossing the cultivar S52-U3 with itself or another soybean plant. The invention also relates to soybean cultivar S52-U3 further comprising one or more single gene traits, and to methods of producing a soybean having such traits by transformation or mutagenesis. The invention also includes using the soybean cultivar S52-U3 to produce other soybean cultivars or breeding lines.