Both nitrogen and sulphur are important macronutrients necessary for the proper development and yield of soybean. Moreover, sulphur plays a special role in nitrogen metabolism in the plant, and sulphur deficiency leads to a reduction in the utilization of nitrogen from fertilizer. The objective of this study was to assess the effect of nitrogen and sulphur application on the yield and quality traits of soybean seeds. The following factors were analyzed in the experiment: I. Nitrogen application rate: 0, 30 and 60 kg ha−1 applied at different times (before sowing and/or at the start of the seed filling stage); II. Sulphur application rate: 0 and 40 kg ha−1 applied in two portions: half during the development of lateral shoots and half at the start of flowering. Thus the 14 fertilizer combinations were obtained. Result show that the highest seeds yield was obtained in the combinations with 60 kg N applied ½ before sowing + ½ after emergence (BBCH 73-75) and ¾ before sowing +¼ after emergence. In these combinations, sulphur did not significantly affect seed yield. In the remaining nitrogen application, sulphur application significantly increased the seed yield. Taking into account the yield and the chemical composition of the soybean seeds, fertilization with 60 kg N ha−1 in two portions can be recommended—½ or ¾ before sowing and the remainder during the development of pods and seeds—in combination with sulphur application.