Sure. If the antibiotic doesn't work for whatever the infection he has in his ear, it's possible.
Also, there's more and more research that shows that antibiotics we've been using to cure ear infections don't work any faster than the body itself would cure an infection.
It's also possible that he's feeling pressure from fluid behind his ears that isn't infected yet, or that he's feeling "referred" pain from his throat from the strep infection.
When my kids were little I bought an otoscope from the pharmacy so I could look at their ears myself!