The US official at the consulate in Guangzhou experienced a variety of "physical symptoms" between late 2017 and April this year.
The State Department urged citizens to seek medical counsel if they experience similar symptoms.
US Secretary of State Mike Pompeo said Wednesday that an incident involving a US government employee stationed in China who reported "abnormal sensations of sound and pressure" suggesting a mild brain injury has medical indications that are "very similar" and "entirely consistent" to those experienced by American diplomats posted in Havana.
In the alert, the State Department tells Americans visiting China to be aware of the potential for "unusual acute auditory or sensory phenomena accompanied by unusual sounds or piercing noises".
The symptoms described recall those of U.S. embassy workers in Cuba, believed to be the target of invisible attacks, though the United States embassy in Beijing did not link the case to that in Havana.
In Cuba past year, the USA disclosed that 24 diplomats and their family members had fallen victim to an unsolved mysterious attack that left them with injuries resembling brain trauma.
The employee was sent to the United States for evaluation and treatment.
USA officials in Cuba, and their families, started describing unexplained health problems between November 2016 to August 2017.
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The State Department on Wednesday notified US citizens in China that a government employee suffered a mild brain injury after experiencing abnormal sound and pressure.
The alert said a US government employee in the southern Chinese city of Guangzhou reported "subtle and vague, but abnormal, sensations of sound and pressure".
"We can not at this time connect it with what happened in Havana, but we are investigating all possibilities", a USA embassy official said.
The spokeswoman, Jinnie Lee, said the department is taking the incident "very seriously". "Instead, move to a location where the sounds are not present", the recommendation said.
Last October, the State Department ordered non-essential embassy personnel and the families of all staff to leave Havana, arguing the us could not protect them from unexplained illnesses that have harmed at least 24 Americans.
Of the 21 medically confirmed U.S. victims, some have permanent hearing loss or concussions, while others suffered nausea, headaches and ear-ringing.
The Chinese foreign ministry could not be immediately reached for comment. Officials believe some type of sonic weapon may have been used.