Zinc (Zn) deficiency in basmati rice grown under submerged conditions leads to decrease in yield and nutritional quality. Fertilisation with Zn is a cost-effective and rapid way to increase crop productivity with Zn-enriched grain. A field experiment was conducted with five Zn levels (0, 5, 10, 20 and 40 kg ha⁻¹) for two consecutive years to assess the effects of Zn fertilisation on yield, Zn content and accumulation in basmati rice grown in a Zn-deficient soil. Maximum grain and straw yields were measured with Zn application of 40 kg ha⁻¹, although statistically similar to yields with applications of 10 and 20 kg Zn ha⁻¹. Increases in average yield compared with the control varied from 14.8% to 27.7% for grain and from 20% to 33.5% for straw with Zn application treatments. Accumulation of Zn in basmati rice grains was highest with Zn application of 40 kg ha⁻¹, although not significantly different from accumulation with 10 and 20 kg Zn ha⁻¹. Indexes of Zn use efficiency were as follows: agronomic efficiency 21–88 kg kg⁻¹, physiological efficiency 6.93–7.39 t kg⁻¹, grain physiological efficiency 14.95–15.21 t kg⁻¹, apparent recovery efficiency 0.97–4.19%, and utilisation efficiency 6.7–31.0 t kg⁻¹. All of these were higher at lower Zn levels and decreased at increasing levels of Zn. The highest benefit–cost ratio occurred with Zn application of 10 kg ha⁻¹. Therefore, we conclude that Zn application of 10 kg ha⁻¹ was the best treatment in terms of high grain yield, maximum benefit–cost ratio, and Zn accumulation in a Zn-deficient soil.