The application of nitrogen (N) fertilizer deep in soil at the same time as mechanical transplanting of rice seedlings is an effective alternative to conventional broadcasting of fertilizer, but its effects on yields and profitability have not been analysed in detail. Here, we analysed the effects of a side deep application of N fertilizer at transplanting on the N uptake, N use efficiency (NUE), grain yield, and economic profitability of two rice (Oryza sativa L.) cultivars; Yongxian15 (early season) and Yongyou1540 (middle/late season). In the field experiments, two types of N fertilizer (urea (U) and controlled-release urea (CRU)) were surface broadcasted manually (B) or mechanically fertilized at 5.5 ± 0.5 cm soil depth (M) (UB, UM, and CRUM treatments, respectively). The blank control had no N fertilizer (N0). Each N-fertilizer treatment had similar effects on N uptake, grain yield, NUE, and economic profitability in the early, middle, and late seasons. Compared with manually applied fertilizer, mechanically applied fertilizer increased grain yield and NUE in both cultivars. In Yongxian15 and Yongyou1540, the mechanical side deep application of N-fertilizer increased the N recovery efficiency by 62.50-91.57% and 24.38-64.24%, respectively, the N agronomy efficiency by 33.65-63.14% and 22.64-44.70%, respectively; and the grain yield by 6.30-11.64% and 6.23-13.11%, respectively. The CRUM treatments had the highest benefit-cost ratio because of high gross returns and low fertilization costs. The mechanized side deep application of N fertilizer can increase the efficiency and profitability of rice production.