It also found no of criminal wrongdoing by the group's main funder, Arron Banks.
The agency opened an inquiry into Leave.EU after an investigation by the Electoral Commission found that potential offences had been committed.
Responding to the finding, Mr Banks said he would be taking legal action against the Electoral Commission.
But the Commission said that the outcome of the investigation had highlighted "weakness" in electoral law and urged the government to take action to keep foreign money out of UK elections.
The investigation revolved around loans totalling £8 million provided to Leave.EU and the company Better for the Country Ltd (BFTC), which organised the group’s campaign.
In its referral of the case to the NCA last November, the Electoral Commission said it has found “reasonable grounds to suspect” that money given to BFTC via an Isle of Man-based company Rock Holdings came from sources which were impermissible under electoral law, and that Mr Banks and Elizabeth Bilney had concealed the true source of the funds.
But after a 10-month investigation, the NCA found that Mr Banks was legally entitled to take a loan from Rock, a company of which he was the beneficial owner, and legally entitled to release the funds to BFTC.
The NCA found “no evidence that any criminal offences have been committed” under either electoral law or company law.
No further action will be taken against Mr Banks, Ms Bilney, Leave.EU or BFTC, said a spokesman for the agency.
Mr Banks tweeted: "Victory is sweet...No overseas money was used in the Brexit campaign, it was my money. We intend to issue a claim against the EC for the decision to refer this matter to the NCA publicly. We calculate the losses [to be] well over £10m..."
An Electoral Commission spokesperson said: “We are concerned about the apparent weakness in the law, highlighted by this investigation outcome, which allows overseas funds into UK politics. We have made recommendations that would tighten the rules on campaign funding and deter breaches. We urge the UK’s governments to act on those recommendations to support voter confidence.
“Significant sums were spent on campaigning at the 2016 EU referendum and it is vital that voters have transparency over the way these campaigns were funded. It is therefore right that suspected offences are investigated by the appropriate authorities, as the NCA has done in this case.”
Brexit Party leader Nigel Farage said: "I am pleased that the NCA have cleared Arron Banks. The appalling establishment campaign against Mr Banks must now end. Heads must roll - beginning with the Electoral Commission who, without evidence, suggested that criminal offences may have been committed. Disgusting."
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