Hoang Tung bought the 256GB version of that model in the popular desert titanium color, which was sold out at most retailers.
A carton containing his phone in its original packaging was shipped to him last Saturday afternoon by Giao Hang Tiet Kiem, which handles most deliveries for the online Apple store.
Tung was suspicious to find that the package was light though there were signs it had been opened, which prompted him to film the unboxing process.
He found the iPhone box inside had been opened, as evidenced by its seal being broken, and the phone was missing.
Tracking the serial numbers on the original packaging, he discovered that the phone had been activated two days before he received the box.
He notified the delivery firm, who said it had reported the case to Apple and would offer him a solution after the weekend.
Apple later contacted him and said it would send him a phone plus a voucher worth VND1 million to be used at its online store. They are expected to be delivered early next month.
Tung said he was glad Apple handled the issue quickly, but disappointed he has a long wait ahead.
"I wanted to get the phone early and I do not care much about the voucher. If I knew I was going to get the phone late, I would have bought it from a retailer instead of ordering from Apple's website."
Apple and the delivery firm have not said why the package was empty, but the latter said it would report to the police if there are indications of unlawful activities.
Shipping expensive devices in Vietnam is fraught with risk, according to electronics store owners.
Le Binh, who runs a shop selling cameras in Hanoi, said he once sent a product worth VND70 million to a customer in HCMC, who ended up receiving a brick.
The store took a long time to resolve the issue but only received partial compensation from the shipping firm because it had not bought insurance for the package.
Minh Hai, who sells electronic products online in Hanoi, said nonetheless buyers are almost always protected in these cases if they provide video evidence that the package was tampered with.