Zinc (Zn) is an important micronutrient for rice (Oryza sativa L.) production and its deficiency has been observed in various production systems. High grain Zn concentration is equally important for high rice yield and human health. In this work, the effects of Zn fertilization on seedling growth, grain yield, grain Zn concentration, and their association with root traits were studied under alternate wetting and drying (AWD), aerobic rice (AR), system of rice intensification (SRI), and continuous flooding (CF). Zinc fertilization (15 kg ha−1) improved nursery seedlings chlorophyll and Zn concentrations, root length, and number of roots with highest values observed in CF. At harvesting, maximum plant height, panicle length, total and panicle bearing tillers, and kernel yield were found with Zn addition in AWD and CF rice systems. Mid season drainage provided at maximum tillering and Zn fertilization increased its concentration in leaves, culms, panicles, and grains under CF and AR at physiological maturity. Most of Zn applied was allocated into culms and panicles, nevertheless, a significant increase in grain Zn concentration was also observed in all production systems. Association of leaf Zn with grain Zn concentration was stronger than with culm and panicle Zn. The results indicate that Zn application after rice nursery transplanting is more important for grain Zn enrichment in all rice systems than for increase in grain yield in all systems except AWD where grain yield was also increased. More grain yield in CF and AWD as compared to SRI and AR can also be attributed to decreased spikelet sterility and to better Zn phyto‐availability in these rice systems at physiological maturity.