Local media reported that the Mingo County health department ordered the Pizza Hut in Kermit, about 85 miles southwest of Charleston, to shut down.
Pizza Hut Corp. released a statement saying it was "embarrassed" by the manager's actions. The company says it has "zero tolerance" for violations of its operating standards. The employee was fired. His name was not released.
The video shows the manager urinating in a sink in the kitchen.
Pizza Hut says the incident occurred after business hours.
County health official Brett Vance says the restaurant is closed until it is thoroughly cleaned and there are reassurances of safeguards in place.