The Issaquah, Wash., company said changes in gas prices and foreign exchange rates hurt revenue from stores open at least a year for the five-week period that ended April 7.
Analysts expected, on average, that revenue from stores open at least a year would rise 5.2 percent, according to Thomson Reuters.
Revenue at stores open at least a year is a key gauge of a retailer's health because it excludes results from stores recently opened or closed.
The wholesale club operator said revenue from established U.S. locations climbed 5 percent, while international sales rose 2 percent. Not counting the effect of gas and foreign exchange rates, revenue from stores open at least a year increased 6 percent.
Total revenue for that period climbed 7 percent to $9.67 billion compared to the same period last year.
The company currently runs 626 warehouses, including 449 in the United States and Puerto Rico, 85 in Canada and 33 in Mexico.
Costco said last month its fiscal second-quarter net income climbed 39 percent, topping Wall Street expectations, as it pulled in more money from membership fees, sales improved and it recorded a large tax benefit. The company earned $547 million, or $1.24 per share, for the period that ended Feb. 17 on $24.87 billion in revenue.
Its shares finished at $102.56 per share on Wednesday. Its shares set a 52-week high of $107.75 on April 2.