Site-specific nutrient management (SSNM) can be an alternative to a recommendation for uniform fertilizer use across a rice (Oryza sativa L.) production system within a country or region of a country. We developed a web-based decision support tool named Nutrient Manager for Rice (NMR), which used principles of SSNM to calculate fertilizer N, P, and K rates for individual fields based on a target yield set for each field. It also used expected growth duration of the rice variety, crop establishment method, and age of transplanted seedlings to calculate days after rice establishment for each of three applications of fertilizer N. NMR enabled P rates to match estimated removal of P with harvested grain and crop residue for the target yield set for each field. We compared field-specific fertilizer recommendations from NMR with uniform application of fertilizer provided by an existing blanket fertilizer recommendation for irrigated inbred rice (BFR) and farmer’s fertilizer practices (FFP) in on-farm trials conducted in 74 irrigated rice fields across three growing seasons in the Cauvery Delta, Tamil Nadu, India. Grain yield was 0.6–0.7 Mg ha−1 higher (P ≤ 0.05) with NMR than FFP in two of the three seasons, even though total fertilizer cost was comparable or less with NMR. Yield was comparable for NMR and BFR, but NMR reduced fertilizer N and P rates and total fertilizer cost compared to BFR. Use of NMR rather than BFR also had less risk of financial loss for a farmer. The likelihood of financial loss with a switch from FFP to BFR averaged 31%. It reduced to 18% with a switch from FFP to NMR. NMR facilitated the calculation of field-specific fertilizer N, P, and K management practices, which increased fertilizer use efficiency without loss in rice yield compared to a recommended uniform fertilizer management across fields.