The post, which appeared to be a quote taken from Fox News, sought to perpetuate an argument - often used by supporters of the president - which seeks to shift focus from the investigation into his presidential campaign's links to Russia on to unfounded speculation around the FBI, Department of Justice (DoJ) and his rival Ms Clinton.
"'We have found nothing to show collusion between President Trump & Russia, absolutely zero, but every day we get more documentation showing collusion between the FBI & DOJ, the Hillary campaign, foreign spies & Russians, incredible' @SaraCarterDC @LouDobbs," Mr Trump wrote.
He followed up four minutes later with another post that retweeted his assistant Dan Scavino, with a picture of him signing an executive order designating "'Patriot Day 2018' to honor the memories of the nearly 3,000 lives lost on September 11, 2001".
The US president included the hashtags #NeverForget and #September11.
Mr Trump next launched a renewed attack on the FBI and the DoJ, which he said were doing "nothing" to look into an alleged "media leak strategy" by two FBI agents investigating links between the Trump campaign and Russia.
New Strzok-Page texts reveal “Media Leak Strategy.” @FoxNews So terrible, and NOTHING is being done at DOJ or FBI - but the world is watching, and they get it completely.— Donald J. Trump (@realDonaldTrump) September 11, 2018
"Eric Holder could be running the Justice Department right now and it would be behaving no differently than it is," Mr Trump continued, quoting one of his favourite Fox News presenters, Lou Dobbs.
Eric Holder is a former Democratic attorney general appointed by former president Barack Obama in 2009.
Mr Trump later tweeted in praise of his lawyer Rudy Giuliani, who was mayor of New York City at the time of the terrorist attacks.
"Rudy Giuliani did a GREAT job as Mayor of NYC during the period of September 11th. His leadership, bravery and skill must never be forgotten," Mr Trump wrote. "Rudy is a TRUE WARRIOR!"
In 2013, three years before he became president, Mr Trump sparked anger after using the 9/11 anniversary to reference "haters and losers".
"I would like to extend my best wishes to all, even the haters and losers, on this special date, September 11th," he posted on Twitter.
“@realDonaldTrump: I would like to extend my best wishes to all, even the haters and losers, on this special date, September 11th.”— Donald J. Trump (@realDonaldTrump) September 12, 2013
It is just one of a litany of questionable comments the US president has made about 9/11.
On the day of the attacks, Mr Trump noted his skyscraper, at 40 Wall Street, went from being the second-tallest in downtown Manhattan to the tallest, following the collapse of the Twin Towers.
In 2015, Mr Trump claimed when talking about Muslims that "thousands of people were cheering" in Jersey City, situated across the Hudson River from lower Manhattan, as the towers fell. There is no evidence of mass celebrations there by Muslims.
Three months later, he said he lost "hundreds of friends" in the attack, but failed to provided any names, other than mentioning knowing a Roman Catholic priest who died while serving as a chaplain to the city fire department.
Despite Mr Trump's apparent preoccupation into the Russia investigation, on Tuesday he visited a Pennsylvania field that became a 9/11 memorial.
Mr Trump and his wife, Melania, were due participate in a remembrance in Shanksville, where a California-bound commercial airliner crashed after the 40 passengers and crew members learned what was happening and attempted to regain control of the plane. Everyone on board was killed.
Nearly 3,000 people died on 9/11 when other planes were flown into New York's World Trade Center and the Pentagon in an attack planned by al-Qaida leader Osama bin Laden. Nearly a decade later, bin Laden was killed in May 2011 during a US military operation ordered by Mr Obama.
Shortly before he was due to deliver a speech at Shanksville, Mr Trump tweeted: "17 years since September 11th!"
17 years since September 11th!— Donald J. Trump (@realDonaldTrump) September 11, 2018
White House press secretary Sarah Huckabee Sanders said of Mr Trump's visit to Shanksville: "Certainly the focus will be on remembering that horrific day and remembering the lives that were lost, and certainly honouring the individuals who were not only lost that day, but also put their lives of the line to help in that process."
Mr Trump was in his Trump Tower penthouse — 4 miles from the World Trade Center — during the 2001 attacks.
Additional reporting by AP