Nitrogen (N) fertilizer split-application is the most widely adopted N management in rice production. To investigate the genotypic differences in the uptake of fertilizer-N applied at different growth stages and in the partitioning of accumulated N in transplanted rice, a two-year field experiment using a split–split plot design with two N rates (105 and 210 kg ha) and three N-labelled fertilizer application treatments was conducted in three rice varieties with different fertilizer-N recovery efficiencies (FNREs). The FNRE of total fertilizer was measured, and the FNREs of basal, tillering and panicle fertilizations were analyzed by applying N-labelled urea as basal, tillering or panicle fertilizer. Although the panicle-FNRE (32%-68%) was greater than the FNREs of both basal and tillering fertilizers (10%–36% and 13%–42%, respectively), the FNRE of total fertilizer was significantly and positively correlated with both basal and tillering-FNREs (p < 0.01). The high-FNRE varieties absorbed more basal fertilizer-N compared with the low-FNRE variety and had significantly greater basal-FNRE and percentages of basal fertilizer-N in the stems at heading and in the panicles at maturity. Early and quick tillering emergence was observed in the high-FNRE varieties, and there was a significant positive relationship between basal-FNRE and tillering rate. The above results indicate that the difference in basal fertilizer-N absorption plays an important role in the genotypic difference in FNRE, and high-FNRE varieties might be selected from the varieties characterized by fast tillering in the early growth stages.