Primary fungal sinusitis was identified in 5 horses displaying signs of headshaking. All 5 horses had fungal plaques adhered to the infraorbital canal (IOC). Headshaking signs were exhibited by 3 horses prior to treatment and 2 horses after treatment. Standing computed tomography (CT) identified erosion of the IOC in the 2 cases in which it was performed. Fungal culture and PCR identified 3 species of fungi, Rhizomucor pusillus, Scedosporium apiospermum and Aspergillus nidulans which have not previously been described as a cause of sinusitis in horses. Surgical debridement followed by topical antifungal therapy was used in all 5 horses. Recurrence of the fungal plaques in 4 horses necessitated further treatment. The headshaking signs and nasal discharge resolved in 3 horses allowing a return to their previous use. Two horses developed persistent headshaking signs despite multiple treatments. Primary fungal sinusitis should be considered as a cause of headshaking signs in horses, due to a suspected trigeminal neuropathy. Computed tomography is valuable in identifying erosion of the IOC which is not identified with conventional radiography. Three out of the 5 cases were treated successfully but permanent resolution of the fungal infection is difficult to achieve once the bone overlying the infraorbital nerve has been eroded.