Fusarium species contribute to the development of onychomycosis, one of the most damaging nail diseases. This study aims to evaluate the anti-Fusarium potential of three agents: voriconazole (VRC), ciclopirox olamine (CPO), and thymol, across varied experimental methods, including standard Sabouraud medium, non-nutritive medium supplemented with horn powder, bovine horn slices, and human nail fragments. In the standard Sabouraud medium, 100% mycelial growth inhibition was achieved with VRC, CPO, and thymol at concentrations of 32 μg/mL, 64 μg/mL, and 250 μg/mL, respectively, corresponding to their minimal inhibitory concentrations (MICs). These MICs were tested in a non-nutritive medium supplemented with horn powder, showing that VRC maintained the same antifungal activity. Thymol then reached 44.44% mycelial growth inhibition, while CPO inhibited mycelial growth by only 5.55%. Based on the MICs obtained in standard Sabouraud medium, we also tested MIC, MIC × 2, and MIC × 4 concentrations on bovine horn slices. At MIC × 4, VRC inhibited mycelial growth by 58.1%, followed by thymol, which inhibited mycelial growth by 43.98%, and CPO inhibited mycelial growth by 16.74%. These MIC × 4 concentrations were applied as treatments to human nail fragments. The kinetic test revealed that thymol reduced mycelial growth by 100% after just 2 h of treatment exposure, whereas VRC and CPO failed to reach complete inhibition in the same time window. These findings further demonstrate that the effectiveness of different antifungal drugs may vary depending on the experimental model employed, highlighting the importance of using complementary assays when evaluating potential treatments for onychomycosis.