A 28‐year‐old Icelandic horse gelding was presented with a laryngopharyngeal squamous cell carcinoma. The gelding had been treated for penile carcinoma in situ with a partial phallectomy 2 years earlier. Polymerase chain reaction of tumour DNA and subsequent amplicon sequencing revealed that the equine papillomavirus type 2 E6 oncogene sequences of both lesions were identical. There is strong evidence that equine papillomavirus type 2 is causally associated with genital squamous cell carcinomas and precancerous lesions. Recent reports indicate that equine papillomavirus type 2 might also play an active role in the pathogenesis of approximately 20% of equine squamous cell carcinomas in the oronasal, pharyngeal and laryngeal regions. To the authors’ knowledge, this is the first report of a horse consecutively developing a penile carcinoma in situ and a laryngopharyngeal squamous cell carcinoma that were apparently induced by the same equine papillomavirus type 2 variant. Possible equine papillomavirus type 2 infection pathways in this horse and the importance of early detection of lesions are discussed in this context.