Biomass pellets are emerging as a cleaner alternative to traditional biomass fuels. The potential benefits of using biomass pellets include improving energy utilization efficiency and reducing emissions of air pollutants. To assess the environmental, climate, and health significance of replacing traditional fuels with biomass pellets, it is critical to measure the emission factors (EFs) of various pollutants from pellet burning. However, only a few field measurements have been conducted on the emissions of carbon monoxide (CO), particulate matter (PM), and polycyclic aromatic hydrocarbons (PAHs) from the combustion of pellets. In this study, pine wood and corn straw pellets were burned in a pellet burner (2.6 kW), and the EFs of CO, organic carbon, elemental carbon, PM, and PAHs (EF(CO), EF(OC), EF(EC), EF(PM), and EF(PAH)) were determined. The average EF(CO), EF(OC), EF(EC), and EF(PM) were 1520 ± 1170, 8.68 ± 11.4, 11.2 ± 8.7, and 188 ± 87 mg/MJ for corn straw pellets and 266 ± 137, 5.74 ± 7.17, 2.02 ± 1.57, and 71.0 ± 54.0 mg/MJ for pine wood pellets, respectively. Total carbonaceous carbon constituted 8 to 14% of the PM mass emitted. The measured values of EF(PAH) for the two pellets were 1.02 ± 0.64 and 0.506 ± 0.360 mg/MJ, respectively. The secondary side air supply in the pellet burner did not change the EFs of most pollutants significantly (p > 0.05). The only exceptions were EF(OC) and EF(PM) for pine wood pellets because of reduced combustion temperatures with the increased air supply. In comparison with EFs for the raw pine wood and corn straw, EF(CO), EF(OC), EF(EC), and EF(PM) for pellets were significantly lower than those for raw fuels (p < 0.05). However, the differences in EF(PAH) were not significant (p > 0.05). Based on the measured EFs and thermal efficiencies, it was estimated that 95, 98, 98, 88, and 71% reductions in the total emissions of CO, OC, EC, PM, and PAHs could be achieved by replacing the raw biomass fuels combusted in traditional cooking stoves with pellets burned in modern pellet burners.