Bexar County Elections Administrator Jacque Callanen said the incident happened Thursday night as polls were about to close.
The election clerk who was assaulted received medical attention on-site and later went home, officials said.
The elections administrator did not say what led up to the assault.
"We said just be pleasant," Callanen said. "We're asking that more and more and more because as the lines are getting long, obviously people are getting a little more testy for standing in a line. We understand, but the officials are doing a fantastic job, and they don't need to be treated like that.
It's unclear if anyone will face charges over this incident.
The early voting site was back open on Friday but a law enforcement officer is posted at that polling location.