(1→3)-β-D-glucan is a major component of the fungal cell wall. It is commonly used to evaluate human exposure to fungi. A personal sampling system was developed to size-selectively evaluate the workplace protection factors (WPFs) of N95 filtering facepiece respirators (FFRs) and surgical masks (SMs) against fungi. This field study was performed with human subjects wearing an N95 FFR or a SM during farming activities. The geometric means of the WPFs of N95 FFRs and SMs were 156.2 and 12.2 for the total culturable fungi, 55.4 and 9.0 for the total fungi, and 10.5 and 11.1 for (1→3)-β-D-glucan. The WPFs for N95 FFRs against fungal contaminants were mostly greater than those for SMs; however, about 4.8%–35.0% of WPFs in the spore size range > 1.8 µm were still below 10 (the assigned protection factor designated for N95 FFRs by the US Occupational Safety and Health Administration). The WPFs of N95 FFRs and SMs against culturable fungi and (1→3)-β-D-glucan increased with the particle size. The total (1→3)-β-D-glucan significantly correlated with the total fungi (r = 0.588, p < 0.001) and total culturable fungi (r = 0.463, p = 0.002), which suggests that (1→3)-β-D-glucan can be used as an indicator to assess respiratory protection against airborne fungi on agricultural farms.