This study aimed to optimize and validate methods for the analysis of thiamin and folic acid in fortified rice, pure and mixed to the milled rice (raw and cooked). The analysis was performed by high-performance liquid chromatography coupled to a diode array detector (HPLC—DAD). Different mobile phases were tested. Different ratios of organic modifier, pH ranges, triethylamine concentrations, and flow rates were used. For the validation, tests of recovery, repeatability, linearity, limit of detection (LOD), and limit of quantification (LOQ) were performed. The optimized methods showed good resolution of vitamins’ peaks, excellent recovery (82.6 to 104%), repeatability with relative standard deviation of peak areas, and retention times less than 10% and high coefficients of determination (0.9998 for thiamin and 0.9997 for folic acid). The LOD and LOQ were 0.00193 μg and 0.0193 μg for thiamin and 0.000934 μg and 0.00934 μg for folic acid. The optimized methods demonstrated reliability and sensitivity in the detection and quantification of these vitamins in fortified rice, pure and mixed to milled rice (raw and cooked). Furthermore, the methods were performed in isocratic mode, with short run time (<13 min), reflecting positively on the economy of reagents and analysis times.