Clinton came under fire frequently throughout the campaign over her own email scandal and the Clinton Foundation, so it's interesting she would weigh in on a topic of this nature.
The elder Flynn subsequently deleted another fake news story about Clinton from his Twitter feed, one that falsely claimed the Federal Bureau of Investigation had evidence "to put Hillary and her crew away for life".
Flynn made numerous phone calls to the Russian Ambassador to the United States before Trump took office, and later hinted he may have gone against diplomatic protocol by discussing the rollback of sanctions.
The debunked conspiracy theory alleged that the Clintons were connected to a child-sex ring that was run out of a DC-area pizza shop. Yet, Flynn Jr. says his father's integrity has been tainted by "disinformation".
He stepped down Monday after admitting that he had given "incomplete information" to Vice President Mike Pence and others about a telephone call he shared with the Russian ambassador in late December.
Clinton's response to Flynn's resignation harks back to the 2016 presidential election days of "Pizzagate", a odd, quickly debunked conspiracy theory.
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Hillary Clinton has spent her entire career having to be buttoned up.
Clinton referenced all this in a wry message early Tuesday, in which she retweeted a joke by Philippe Reines, who worked for Clinton in both the Senate and State Department.
The White House has said it will replace Mr Flynn with retired Army Lt. Gen. Joseph K Kellogg Jr as acting national security adviser.
"Philippe's got his own way of saying things", Clinton tweeted, "but he has a point about the real consequences of fake news".
He then posted a link to Dominos' jobs page, and signed it, "xo Philippe".
This isn't the first time Clinton has thrown shade on Twitter in recent days; the former First Lady also succinctly celebrated the take-down of Trump's travel ban executive order in a Seattle court. I for one am hoping she does.