Ruth Johnson, 33, who has two children, including a month-old baby, had not been using her usual method of contraception with her fiancée.
She went to the Tesco dispensary in Hewitts Circus, Cleethorpes, Lincs, and asked an as assistant for the pill Levanelle.
Miss Johnson was told it could only be dispensed by the locum pharmacist who was called to speak with her.
She said: "He came out from behind a screen and told me that he would not be allowing me to buy the pill from him because he had a right to refuse to sell it on the basis of his personal beliefs.
"The pharmacist was of Asian origin so I asked him if it was because of his religion and he replied 'Yes'."
Miss Johnson, from Cleethorpes, was left feeling ashamed and worried and complained to the store manager who told her they couldn't force the pharmacist to sell the product.
She said: "I asked him if a Jewish or Muslim checkout operator could refuse to sell pork or alcohol or if a Jehovah's Witness could refuse to sell birthday and Christmas cards."
Her concern is that the policy could deter teenage girls from seeking the morning-after pill.
"I appreciate we live in a multi-cultural society but what gives him the right to impose his beliefs onto me?" she added.
A Tesco spokesman said the pharmacist was acting within his rights to refuse to sell the pill and the customer was advised where else she could buy the product.