President-elect Joe Biden’s choice for secretary of state, Antony Blinken, has said he agrees with the finding.
Rights groups believe that China has detained up to a million Uighurs over the past few years in what the state defines as “re-education camps”.
BBC investigations suggest that Uighurs are being used as forced labour.
Tensions with China have been a defining feature of Mr Trump’s term, from trade policies to the coronavirus pandemic.
“I believe this genocide is ongoing, and that we are witnessing the systematic attempt to destroy Uighurs by the Chinese party-state,” Mr Pompeo said in a statement. It is his last day in office as part of Donald Trump’s administration.
While the statement puts pressure on China, it does not automatically introduce any fresh penalties.
Mr Blinken was asked at his confirmation hearing on Tuesday if he agreed with Mr Pompeo’s announcement, to which he answered: “That would be my judgment as well.”
Mr Biden’s team made a similar allegation last August, saying the Uighurs had suffered “unspeakable oppression… at the hands of China’s authoritarian government”.
China says it is fighting “three evil forces” of separatism, terrorism, and extremism in the far western region of Xinjiang, where most of the 11 million Uighurs live. It says its “training measures” in Xinjiang are necessary to combat these.
In recent years, Xinjiang has seen a large influx of settlers from China’s ethnic Han majority. Anti-Han and separatist sentiment has become more prevalent in the territory since the 1990s, flaring into violence on occasion.
Campaigners say China is trying to eradicate the Uighur culture, by forcing Muslims to eat pork and drink alcohol.
Last week, Mr Trump’s administration banned the import of cotton and tomato products from the Xinjiang region of China, where the majority of Uighurs live.
Xinjiang accounts for nearly a fifth of world cotton production, the US estimates.
China has been widely accused of using detention camps in Xinjiang for forced labour, particularly in the cotton industry.
An investigation by the BBC in 2019 suggested that children in Xinjiang were being systematically separated from their families in an effort to isolate them from their Muslim communities.
Recent research shows Uighur women have been forcibly subjected to methods of birth control.
China denies using forced sterilisations in Xinjiang. (Courtesy BBC)