Still, this is up from the 35.2 million iPhones sold in the year-ago quarter, no doubt owing to the popularity of the iPhone 6 and iPhone 6 Plus.
Cook also said during the earnings call that "Android switchers are at an all-time high", following reports that a third of iPhone buyers in Europe switched from Google's rival operating system.
Mac sales were also up, coming in at 4.7 million for the three-month period compared with 4.4 million in the year-ago quarter, and 4.5 million in Q2, adding weight to IDC's recent report placing Apple as the world's fourth largest PC maker.
Apple Macbook Pro with Retina display 2014
Apple's Q3 results don't paint such a pretty picture for the iPad, which sold 10.9 million units during the quarter, down from 13.27 million this time last year and 12.6 million in the previous quarter.
However, Cook seemed pretty pleased with the numbers, and lauded the fact that App Store revenues grew 24 percent during the three-month period to $5bn.
"We had an amazing quarter, with iPhone revenue up 59 percent over last year, strong sales of Mac, all-time record revenue from services, driven by the App Store, and a great start for Apple Watch," he said."