A jury in San Francisco found him not guilty on all counts, in a stunning victory for Mr Lynch. He had been accused of inflating the value of his company, Autonomy, ahead of its sale.
Lynch could face more than 20 years in prison if convicted, denied the charges, and, unlike other American multi-millionaires, took the stand to defend himself.
In his testimony, he maintained he had focused on technology, not accounting, distancing himself from other executives, including the company's former chief financial officer, who was already successfully prosecuted for fraud.
Lynch told the press he was elated with the verdict and grateful to the jury for their attention to the facts over the last 10 weeks.
"I am looking forward to returning to the UK and returning to what I love most: my family and innovating in my field."
University of Cambridge graduate Mr Lynch co-founded Autonomy in 1996 from a specialist software research group called Cambridge Neurodynamics.
He led it as it became one of the UK's biggest companies, winning him comparisons to Microsoft's Bill Gates and Apple's Steve Jobs.
The company, known for software that could extract useful information from "unstructured" sources such as phone calls, emails or video, was ultimately sold to Hewlett-Packard (HP) in 2011 in a deal that ranked as the largest-ever takeover of a British technology business.
Lynch made £500 million from the sale. Just a year later, HP wrote down the value of Autonomy by $8.8 billion.
Years of legal battles followed.
The company's chief financial officer, Sushovan Hussain, was found guilty of fraud in 2018 and sentenced to five years in prison.
US prosecutors charged Lynch in 2018, accusing him of inflating the firm's value by using backdated agreements to mislead about the company's sales, concealing the firm's loss-making business of reselling hardware, and intimidating or paying off people who raised concerns.
Lynch was eventually extradited after a UK judge ruled in favour of HP in a similar civil fraud case in 2022. HP is seeking a reported $4 billion in that case.
Lynch, a former UK government adviser who sat on the boards of the BBC and the British Library, had faced house arrest in the US while preparing for the trial, which began in San Francisco in March.
Prosecutors had called dozens of witnesses to the stand, including the former head of HP Leo Apotheker, who was fired shortly after the purchase was announced.
But the arguments fell flat. Lynch's team argued that HP had failed to vet the deal correctly and mismanaged the takeover, while he testified he was uninvolved with the described transactions.
Judge Charles Breyer had already dismissed one count of securities fraud during the trial for lack of evidence.
Abraham Simmons, a US Attorney's Office spokesman, said: "We acknowledge and respect the verdict.
"We would like to thank the jury for its attentiveness to the government's evidence in this case."
In addition to Lynch, another former finance executive at Autonomy, Stephen Chamberlain, was also on trial. He was found not guilty.
Lawyers for Mr Lynch, Christopher Morvillo, and Brian Heberlig said in a statement that they were thrilled by the outcome, which reflected a "rejection of the government's profound overreach in this case."
"This verdict closes the book on a relentless 13-year effort to pin HP's well-documented ineptitude on Dr Lynch," they said. "Thankfully, the truth has finally prevailed."