The 15-year-old boy, from Flintshire, north Wales, broke out with lesions on his hands, feet and arms after feeding calves on his family farm.
Photos show pus-filled lumps on the teenager's body caused by the virus more common in the 18th Century.
Public Health Wales say the last reported human case in the country was 10 to 15 years ago.
The boy's mum, who says her son does not want to be named, said: "We were really unsure what it was.
"The one on his ankle was worrying – it was weeping a clear liquid down his ankle.
"My son was quite embarrassed – it looked quite a mess, the lesions weren't nice and it wasn't pleasant for him.
"It took weeks and weeks to go, a long time. He still has some marks on his hands."
After seeing his GP the teenager was sent straight to the Countess of Chester Hospital and diagnosed with cowpox.
Dr Aysha Javed, who diagnosed the teenager, said: "I think the boy and his family were quite bemused when we told them – I don't think they expected that to be the diagnosis."
Cowpox was more common in the 18th Century when milking maids often caught it.
The virus, which is not contagious from person to person, has almost disappeared because fewer people milk cows by hand.
The teenager was diagnosed about three months ago. His case came to light when Dr Javed and her colleagues alerted other medics to it during a recent European Society for Pediatric Dermatology annual meeting.
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