It is well known that nodulation and nitrogen fixation of soybean are generally depressed by the application of N fertilizers. We previously reported that a new fertilization method consisting of deep placement of slow‐release N fertilizers, such as coated urea and lime nitrogen (calcium cyanamide) at a 20 cm depth enhanced soybean growth and seed yield. In the present study, the effect of deep placement of various 15N‐labeled N fertilizers (100 kg N ha−1) was compared in converted paddy fields located at Niigata Agricultural Research Institute, in Nagaoka. Fertilizers consisting of 15N‐labeled ammonium sulfate (AS), urea (U), coated urea (CU) or lime nitrogen (LN) were applied at a 20 cm depth for nodulated soybean (cv. Enrei) and for a non‐nodulated isogenic line (En1282). The plants without deep placement of N fertilizer were used as control (Cont) for both Enrei and En1282. Whole plants were sampled at maturing stage, and 15N abundance and N concentration in each part were determined. The evaluation of the amounts of Ndfa, Ndfs and Ndff was conducted by the 15N dilution method using En1282 as a reference plant. Also the amounts of Ndfa and Ndfs+Ndff were estimated by the N balance method for comparing Cont and the other treatments. In all the deep placement treatments, the non‐nodulated line exhibited only 36–40% of total dry weight and 16‐30% of total N accumulation compared with the nodulated line, due to N deficiency associated with the lack of nitrogen fixation. In both nodulated and non‐nodulated soybeans, plant growth and the total amount of accumulated N showed the highest values by the application of LN, followed by CU, U, AS and Cont, respectively. The value of the seed dry weight of Enrei was highest in the LN (73 g plant−1), followed by CU (63 g plant−1), U (47 g plant−1), AS (37 g plant−1) and Cont (26 g plant−1) treatments. The value of Ndfa estimated by the 15N dilution method was higher in the LN (3.6 g N plant−1) and CU (2.8 g N plant−1) treatments than in the U (2.3 g N plant−1) and AS (2.2 g N plant−1) treatments. In addition, the value of Ndfa estimated by the N‐balance method was also higher in the LN (4.1 g N plant−1), CU (3.9 g N plant−1), U (2.8 g N plant−1) and AS (2.6 g N plant−1) treatments than in the Cont treatment (1.5 g N plant−1). The recovery rate of N fertilizers in Enrei was higher in the LN (43%) and CU (36%) treatments than in the U (21%) treatment and lowest in the AS (8.5%) treatment. These results indicate that deep placement of LN and CU is effective to improve soybean growth and seed yield. The combination of “deep placement” and “slow‐release N fertilizers” is important to supply N until the maturation stage, resulting in the increase of seed yield.