Unichem Botany in Auckland had priced 30 pills of Telfast 180mg at $66.99, while at Unichem at WestCity in Henderson, it was $22 less at $44.99.
Unichem, owned by Green Cross Health, told Consumer NZ that its Botany franchise's pricing was "an anomaly" and the owner is now using the company's $49.99 recommended retail price.
Meanwhile the cheapest pharmacy for one product, charged more for others.
Auckland's Henderson Discount Pharmacy had the best value for Fexaclear (fexofenadine) but it was one of the more expensive places to buy Zyrtec (cetirizine).
When Consumer NZ contacted the store, Henderson said its $45.99 price tag for Zyrtec 30s was a mistake and adjusted it to $31.99.
And a Wellington pharmacy charged its customers $30 for the same drug.
"We were surprised to see such extreme differences in price for the same product, sometimes at outlets belonging to the same chain," said Consumer NZ chief executive Sue Chetwin.
"This demonstrates how important it is for consumers buying antihistamines to shop around."
Of the seven products, four were "generics", with the same active ingredient and effect on the body as big name brands, such as Claratyne (loratadine), Telfast (fexofenadine) and Zyrtec (cetirizine).
Across all 30 pharmacies, the cheapest packet of 30 pills of Telfast 180mg was $44.99.
The most expensive was $22 more ($66.99).
There was a similar price variation for Claratyne 30s - the lowest-priced packet in the survey cost $23.50 and the highest-priced was $44.90.
Looking at the average cost per pill, large-sized packs of generic antihistamines were the best value.
On average, Razene's largest pack (90), worked out to be 48¢ per pill compared with $1.30 a pill for Zyrtec's large size (30).
"We found the cheapest prices for five of our seven surveyed products were offered by an online-only pharmacy, even after delivery fees were factored in," Chetwin said.
"Buying online is a good way to cut the cost of your antihistamine bill."