Noman Ansari, who stopped at a branch in Karachi for a diet Coke on Saturday night, said the episode was a symptom of an increasingly intolerant nation.
A spokesman for McDonald’s said it was investigating the complaint.
Mr Ansari said trouble started when he sat next to his wife and slipped an arm behind her shoulder.
A member of staff told the couple to move but when they again sat beside each other in an adjacent booth it became clear that the issue was not their location, but the proximity of a man and a woman in public.
In an account posted on his blog, Mr Ansari said he was told: “Sir, this is a family restaurant. Couples sitting together is against the policy of McDonald’s Pakistan, as it goes against the family atmosphere of the restaurant.”