Brown spot (BS) disease poses a significant threat to rice cultivation globally, impacting millions of hectares annually. Research indicates that the severity of BS is closely linked to abiotic stresses and crop nutrition. A field experiment was conducted using transplanted (TP) and direct-seeded-rice (DSR) crop establishment methods to optimize the effective fungicide and nitrogen dose. The split-plot design was applied to study the effect of two factors (N-dose and fungicides) varying at different levels under two different crop establishment methods (TP and DSR) for two consecutive Kharif seasons (2021 and 2022). The BS severity was measured as the percent disease index (PDI), and the results of two seasons were pooled. The results indicated that all three factors significantly (p = 0.05) influenced the PDI and grain yield. The PDI under different fungicides was higher in DSR (30.20–88.90) than in TP rice (21.64–70.00). Similarly, increased N-dose altered the PDI negatively (p = 0.05) in both TP (32.16–46.12) and DSR (44.35–59.09) methods. The results indicated Tebuconazole 50% + Trifloxystrobin 25% WG (T7) at 125% recommended dose of nitrogen as the best combination, as it recorded the lowest PDI of 21.6 and 30.2 in the TP and DSR, respectively. Similarly, all three factors interacted significantly (p = 0.05) and affected the final grain yield. Overall, the BS is more severe in DSR, and a higher dose of N reduces the BS severity in both TP and DSR. Therefore, N fertilizer management, especially in the DSR, is essential, along with a fungicide, for effective management of the brown spot disease.