Zinc (Zn) deficiency is a major constraint for rice (Oryza sativa L.) production and a global concern for human nutrition. Water scarcity and increasing labour costs are dictating the shift in rice culture from puddling, transplanting and flooding to dry seeding and the use of alternate wetting and drying water management. These changes may affect Zn availability to rice plants. This study was conducted to evaluate the effect of four different Zn application methods on the productivity, profitability, and grain Zn concentration of rice at two different sites (Faisalabad and Sialkot) in Punjab, Pakistan in 2013 and 2014. Zinc was applied as ZnSO4·7H2O either as a (1) basal application to the soil (10 kg Zn ha−1), (2) foliar spray (0.5% Zn solution), (3) seed primer (0.5 M Zn), or (4) seed coating (2 g Zn kg−1 seed). The rice cultivar, Super Basmati, was grown in conventional puddled transplanted flooded (TR) and dry-seeded non-flooded rice (DSR) systems. All Zn application methods increased grain yield of both DSR and TR by around 30% compared with the control (no added Zn). While there were significant differences between the effects of the application methods on grain yield at both sites, the differences were small (≤0.2 t ha−1) and there were no consistent trends, apart from much lower yield with seed coating of TR at Sialkot. All Zn treatments significantly increased grain Zn concentration in both production systems at both sites, apart from seed coating in DSR at Faisalabad. Seed coating consistently gave the smallest increase in grain Zn concentration. Foliar Zn application consistently gave the highest or equal highest grain Zn concentration at Faisalabad, while soil application consistently gave the highest or equal highest concentration at Sialkot. Profitability was greatly increased by all Zn application methods, with net benefit increasing by factors of 1.4–3.1. Foliar application was the most profitable method for TR at both sites, while seed coating was the most profitable method for DSR. At both sites, seed coating produced by far the highest agronomic efficiency and apparent recovery, mainly due to the low amount of Zn applied. In conclusion, all four Zn application methods increased rice paddy yield and profitability at both sites in both TR and DSR. Given the low effectiveness of seed coating in increasing grain Zn concentration, it is recommended that farmers apply Zn to rice by soil application, seed priming or foliar application.