first you have to guse surf to go to a city and there is a phamacy there
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Cianwood Pharmacy.
if you mean the medicine for 'amphy' in the light house, go to the medicine man in cianwood city he will give you a 'secret potion'
Surf to Cianwood City, there is a pharmacy there and the guy inside will give you secret medicine.
building near Pokemon center on cinnabar island
After returning to the sick Pokemon in the light tower (bring your medicine from Cianwood with you).