Experts say the pain is probably occurring because the Glass display is in the least comfortable area of humans' field of vision.
In early prototypes, Google reportedly tried putting the screen in front of the eye and below it, but found that both obstructed the wearer's line of sight.
However, most people are unaccustomed to looking up and to the side for long periods of time, which means overusing Glass may cause a strain to the average eye.
Harvard University optometrist Dr Eli Peli acted as a consultant to Google during the development of the device. He told Betabeat: "The only people who look up a lot are some professionals like electricians and painters. Most of us look either straight or down. It's well known that up is less comfortable."
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Google insists that only a small number of Glass Explorers have complained of headaches, and an FAQ on the Glass website warns, "Like when wearing glasses, some people may feel eye strain or get a headache."
In a statement, the firm added: "Glass is designed for micro-interactions, not for staring into the screen, watching Friday night movie marathons or reading War and Peace."
Dr Peli said that while Glass is intended for brief tasks such as taking a picture or checking directions, new users spend a long time tinkering with the settings and apps on their device, which may lead to ocular discomfort.
As wearers start to use the device as originally intended, and their eye muscles grow accustomed to looking in new directions, the pain will likely disappear.
"The recommendation is to not overdo it when you start," Dr Peli said. "Use it in the recommended way right from the beginning."
- Independent