Microbial inactivation is essential for extending the shelf life of raw milk. Radio frequency (RF) thermal pasteurization has emerged as a promising technology for small-scale dairy processing. This study aimed to determine optimal RF temperature–time conditions, evaluate their effects on milk quality across milk from different species of cows, and assess economic feasibility. Raw milk from Holstein Friesian, Jersey, and Brown Swiss cows was treated using a dielectric heating system (40.68 MHz) at 72–92 °C for 20–100 s. The results were compared with conventional low-temperature long-time (LTLT) pasteurization of untreated milk. The optimal condition was 92 °C for 50 s, reducing the aerobic plate count from 5.80 to 0.69 log CFU/mL (a 5.11 log reduction), with no detection of Staphylococcus aureus, Bacillus cereus, and Escherichia coli. RF treatment did not significantly affect milk composition (p > 0.05), and color changes remained within acceptable limits. Milk stored at 4 °C maintained quality and safety for up to 28 days. Economic analysis indicated a net present value of USD 134,721.78, a benefit–cost ratio of 3.25, and a payback period of 6.8 months, confirming economic feasibility. These findings demonstrate that RF pasteurization can improve processing efficiency and support sustainable dairy production.