(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 workplace protection factors (WPF) provided by N95 filtering facepiece respirators (FFR) and surgical masks (SM) against fungi. This field study was performed with human subjects wearing an N95 FFR or a SM in farming activities. The geometric means (GM) of the WPFs of N95 FFRs and SMs were 156.2 and 12.2 for total culturable fungi, 55.4 and 9.0 for total fungi, and 10.5 and 11.1 for (1→3)-β-D-glucan. WPFs for N95 FFRs against fungal contaminants were mostly greater than those for SMs; however, still about 4.8%–35.0% of WPFs in the spore size range (> 1.8 µm) were 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 increasing particle size. Total (1→3)-β-D-glucan significantly correlated with total fungi (r = 0.588, p < 0.001) and total culturable fungi (r = 0.463, p = 0.002). This indicates that (1→3)-β-D-glucan could be used as an indicator to assess respirator protection against airborne fungi in agricultural farms.