The 40-year-old strip, which appears in about 400 newspapers, previously has dealt with controversial subjects such as teenage pregnancy, capital punishment, cancer and alcoholism.
Batiuk told the Harrisbug (Pa.) Patriot-News, which runs "Funky Winkerbean," he was inspired to write his latest series of strips by a news story about parents who opposed a high school's decision to allow a same-sex couple to attend the prom.
"Apparently the school was a little more tolerant than these people wanted," he said. "I was contrasting it in my own mind with what I see when I go to my old high school. My sense is the younger generation's attitude toward gays is a little more open and accepting than their predecessors."
Batiuk said he was careful not to "proselytize" in his comic strip, which follows a couple of gay teenage boys as they plan to go to the prom together, sparking controversy among some parents, but finding support from the majority of their peers.
"Even on the side where people were being intolerant, I wasn't trying to demonize anybody," he said. "My point is if you can get somebody to think, that's great."