In 1970, Aitken was acquitted at the Old Bailey for breaching section 2 of the Official Secrets Act 1911, when he photocopied a report about the British government's supply of arms to Nigeria, and sent a copy to The Sunday Telegraph and to Hugh Fraser, a pro-Biafran (Nigerian Civil War) Tory MP. As a result of the case he was dropped as the Conservative candidate for the Thirsk and Malton parliamentary constituency.
Aitken was elected as MP for Thanet East in the February 1974 general election, from 1983 he sat for South Thanet. He managed to offend PM Margaret Thatcher by ending a relationship with her daughter, Carol Thatcher, and suggesting that Thatcher "probably thinks Sinai is the plural of Sinus" to an Egyptian newspaper. He stayed on the backbenches throughout Thatcher's premiership, as well as participating in the re-launch of TV-AM, when broadcaster Anna Ford threw her wine at him to express her outrage at both his behaviour and the unwelcome consequent transformation of the TV station.
Aitken wrote a highly confidential letter to Thatcher in early 1980, dealing with allegations that the former Director-General of MI5, Sir Roger Hollis, had been a double agent also working for the Soviet Union. This information had come to Aitken from retired CIA spymaster James Angleton. Espionage historian Chapman Pincher obtained a copy of the letter, and used former MI5 officers Peter Wright and Arthur Martin as his main additional secret sources, to write the sensational book Their Trade is Treachery in 1981. This matter continued being highly controversial throughout the 1980s, and led to Wright eventually publishing his own book Spycatcher in 1987, despite the government's prolonged Australian court attempts to stop him from doing so.
Aitken became Minister of State for Defence Procurement under prime minister John Major in 1992. He was later accused of violating ministerial rules by allowing an Arab businessman to pay for his stay in the Paris Ritz, perjured himself and was jailed. This came about by The Guardian's investigation into his misdeeds conducted under his official government capacity. He sued the newspaper for libel in response, but the case collapsed, and he was subsequently found to have committed perjury during his trial. In 1999, he was sentenced to 18 months in prison, of which he served seven months.
Aitken had previously been a director of BMARC, an arms exporter during 1988–1990. In 1995, a Commons motion showed that while a Cabinet minister he had signed a controversial Public Interest Immunity Certificate (PIIC) in September 1992 relating to the Matrix Churchill trial, and that the "gagged" documents included ones relating to the supply of arms to Iran by BMARC for a period when he was a director of the company.
He became Chief Secretary to the Treasury in 1994, a Cabinet position, but resigned in 1995 following the allegations that he had violated ministerial rules.
He was defeated in the 1997 general election. Within a year he had been appointed as a representative for the arms company GEC-Marconi (part of BAE Systems since November 1999).
On 10 April 1995, The Guardian carried a front-page report on Aitken's dealings with leading Saudis. The story was the result of a long investigation carried out by journalists from the newspaper and from Granada Television's World in Action programme. The Guardian also alleged Aitken as Minister for Defence Procurement, arranged prostitutes for Arab businessmen. Granada's World in Action programme repeated the accusation in a television documentary called 'Jonathan of Arabia'.
Aitken had called a press conference at the Conservative Party offices in Smith Square, London, at 5 p.m. that same day denouncing the claims and demanding that the World in Action documentary, which was due to be screened three hours later, withdraw them. He said "If it falls to me to start a fight to cut out the cancer of bent and twisted journalism in our country with the simple sword of truth and the trusty shield of British fair play, so be it. I am ready for the fight. The fight [is] against falsehood and those who peddle it. My fight begins today. Thank you and good afternoon."
The World in Action film Jonathan of Arabia was transmitted as planned and Aitken carried out his threat to sue. The action collapsed in June 1997 (a month after he had lost his seat in the 1997 general election) when The Guardian and Granada produced, via their counsel George Carman QC, evidence countering his claim that his wife, Lolicia Aitken, paid for the hotel stay at the Ritz Hotel in Paris. The evidence consisted of airline vouchers and other documents showing that his wife had, in fact, been in Switzerland at the time when she had allegedly been at the Ritz in Paris. The joint Guardian/Granada investigation indicated an arms deal scam involving Aitken's friend and business partner, the Lebanese businessman Mohammed Said Ayas, a close associate of Prince Mohammed of Saudi Arabia. It was alleged that Aitken had been prepared to have his teenage daughter Victoria lie under oath to support his version of events, had the case continued.
A few days after the libel case collapsed, World in Action broadcast a special edition, which echoed Aitken's 'sword of truth' speech. It was titled 'The Dagger of Deceit'.
During this time, it emerged that when Aitken was being encouraged to resign, he was chairman of the secretive right-wing think-tank Le Cercle, alleged by Alan Clark to be funded by the CIA.
Aitken was charged with perjury and perverting the course of justice and, after pleading guilty on 8 June 1999 to both offences, was sentenced to jail for 18 months of which he served almost seven months as a custodial sentence. While Aitken was sentenced Mr Justice Scott Baker said Aitken had breached trust inexcusably. Scott Baker told Aitken "For nearly four years you wove a web of deceit in which you entangled yourself and from which there was no way out unless you were prepared to come clean and tell the truth. Unfortunately you were not."
During the preceding libel trial, his wife Lolicia, who later left him, was called as a witness to sign a supportive affidavit to the effect that she had paid his Paris hotel bill, but did not appear. In the end, with the case already in court, investigative work by The Guardian reporters into Swiss hotel and British Airways records showed that neither his daughter nor his wife had been in Paris at the time in question.
Aitken was unable to cover the legal costs of his libel trial and was declared bankrupt. As part of the bankruptcy, his trustees settled legal actions against the magazine Private Eye, over the claims it had made that Aitken was a "serial liar". He also became one of the few people to resign from the Privy Council. Aitken's wife and three daughters turned up to support him when he was sentenced.
Aitken attended the Alpha Course in 1997, which he said stirred his interest in Christianity. He attended the course on further occasions prior to imprisonment. After being imprisoned in 1999, he began to study the Bible, learned Greek, and became a student of Christian theology at Wycliffe Hall, Oxford. This part of his life is covered in two autobiographical works called Pride and Perjury and Porridge and Passion.
Aitken's claim that he had found God was met with some scepticism. Aitken said "In a different era, I'd have been one of the cynics myself. If I'd had a parliamentary colleague who'd got into trouble, gone to jail and come out saying, 'I've found God', I'd have said, 'Oh, how very convenient for him'."
The Guardian might insist that Aitken demonstrate the sincerity of repentance by repaying the whopping legal bill of one-and-half-million pounds he landed on them by his dishonest libel action. He was allowed to drop the case on promising to pay costs, but then escaped from the liability when he declared himself bankrupt and revealed that most of his apparent assets turn out to be conveniently owned by other people. The Guardian still believe he has more resources than he will admit.
In 2000 he said that he would not become a vicar because he considered himself not worthy of the office and "wouldn't like to give dog-collars a bad name".
In 2006 Aitken became honorary president of Christian Solidarity Worldwide.
On 30 June 2018, Aitken was ordained in the Church of England as a deacon by Sarah Mullally, the Bishop of London. Since then he has served as a non-stipendiary minister at St Matthew's Church, Westminster and as a chaplain of Pentonville Prison.
Exactly one year after becoming deacon, on 30 June 2019, Aitken was ordained as an Anglican priest in St Mary's Church, Stoke Newington, also by the Bishop of London.
In early 2004, some constituency party members in Aitken's former seat of South Thanet proposed that he should return as Conservative candidate for the seat in the 2005 general election. This was vetoed by Conservative Party leader Michael Howard.
Aitken later confirmed that he would not attempt a return to Parliament, saying that "The leader has spoken. I accept his judgement with good grace." He denied rumours he was to stand as an independent candidate insisting that he was not a "spoiler".
Aitken later declared his support for the United Kingdom Independence Party (UKIP) a week before the party's equally strong performance as the Liberal Democrats, with both parties winning 12 seats each in the 2004 European elections. On 2 October 2004, Aitken attended the (UKIP) conference and re-iterated his support for the party.
In November 2007, with the approval of senior members of the shadow cabinet, he took charge of a task force on prison reform within Iain Duncan Smith's Centre for Social Justice to help formulate Conservative Party policy. Aitken said this was not part of a political comeback. Conservative spokesmen pointed out that the task force is independent of the party, even though the organisation was run by Iain Duncan Smith. The report 'Locked Up Potential: A Strategy to Reform our Prisons and Rehabilitate our Prisoners was published in March 2009.
In September 2020, it was revealed that the former Speaker of the House of Commons, John Bercow, awarded Aitken a parliamentary pass despite the House of Commons claiming that former MPs who had been sentenced to a period of imprisonment of one year or more were ineligible. In September 2020 Aitken had held a pass continuously since at least December 2015.