He has been convicted on several occasions of possession of cannabis for personal use. He served nine days of a 15-day sentence at Loughan House open prison in County Cavan in 1998, for refusing to pay a fine imposed for breach of the Litter Pollution Act.

In 2001, he hit the headlines when he sent more than 200 cannabis cigarettes to politicians in the Oireachtas, one to each TD and senator, as part of his campaign to have cannabis legalised.

On 28 June 2010, Flanagan was elected as the Mayor of Roscommon County Council. On 27 July 2010, Flanagan was the subject of debate over his refusal to lead the prayer said before council meetings; he said that it would be hypocritical for him, as a non-believer, to lead it. The matter was later resolved by asking the Deputy Mayor Ernie Keenan to say the prayer.

In December 2010, Flanagan proposed that his mayoral allowance should be halved, and many of his other allowances be abolished entirely, in recognition of the financial difficulties that the country and the county were experiencing. The proposal met with a mixed reception from his council colleagues.

Flanagan was elected to represent the Roscommon–South Leitrim constituency in the 31st Dáil in the 2011 general election, one of twenty members of the New Vision alliance of independent candidates. He received 8,925 (18.8%) first preference votes, which enabled him to take the first seat with 12,149 votes on the fourth count, while the two incumbent Fine Gael TDs were elected on the sixth count. Neither of the two Fianna Fáil candidates managed to retain the seat of their retiring party colleague, Michael Finneran.

When he was elected in 2011, Flanagan kept his promise to retain only half of his €92,672 salary and distribute the rest to local projects. He refused to hand it back to the State, claiming it would only be pumped into the banks.

In March 2011, one month after being elected to Dáil Éireann, Flanagan announced that he would cease his smoking of cannabis while in Ireland in order to protect his family and focus on the issues for which he stands. He said he still intended to smoke cannabis when abroad. This followed a formal complaint lodged to the Garda Síochána by a Fianna Fáil councillor from Kilkenny about his cannabis use. Flanagan said that: “…my wife and children are the most important people on the planet to me and I don’t want my kids to witness the Garda calling to the house.” He said he would continue to campaign for the legalisation of cannabis.

In July 2011, Flanagan was linked to an incident in which a Dáil microphone picked up a conversation he had with fellow independent TDs Shane Ross and Mick Wallace. During the exchange the trio appeared to be disparaging the appearance of Fine Gael TD Mary Mitchell O’Connor. Wallace initiated the conversation by saying “Miss Piggy has toned it down a bit today”. Flanagan was heard saying “they’d want to ban her wearing pink” and Ross commented that “she normally wears the most garish colours”.

On 2 November 2011, Flanagan walked out of the Dáil amid a heated disagreement with Minister for Agriculture, Food and the Marine, Simon Coveney over turf-cutting rights. Flanagan had observed that his Fine Gael constituency colleague Frank Feighan had promised before the 2011 general election that he would “sign his name in blood” if that was required in order to oppose a turf-cutting ban, with Coveney responding by saying populism was a dangerous thing. Flanagan then said, “Populism and bondholders. I am leaving the chamber”; Coveney then told him to “go on and walk out in protest”. Flanagan retorted, “My daddy did not give me a seat.” This referred to the fact that Coveney had been elected in a by-election after his father Hugh Coveney TD died in an accident in March 1998.

On 15 December 2011, Flanagan helped launch a nationwide campaign against a proposed household charge being brought in as part of the 2012 Irish budget.

In April 2012, Flanagan stated he would be urging people to vote ‘No’ in the referendum on ratification of the European Fiscal Compact Treaty, on the grounds that Ireland would lose power to bigger countries in the European Union, such as Germany and France. He also stated that Ireland should leave the economic and monetary union (EMU), based on the euro currency.

Flanagan admitted to “atrocious” timing after calling gardaí “corrupt” on television, as thousands of people gathered for the state funeral of murdered garda Adrian Donohoe in Dundalk, County Louth, in January 2013. In early March 2013, Daniel McConnell of the Sunday Independent reported that Flanagan had been issued with a fine of €60 and two penalty points on his driving licence for operating a mobile phone while driving in June 2011. According to these reports, Flanagan then had his punishment rescinded at a later date with a claim of being ‘on Dáil business’. The stories caused controversy at the time, for Flanagan, along with other independent TDs, had been involved in a campaign highlighting the cancellation of 197 Fixed Charge Notices out of the 1.4 million issued, which it was alleged were ‘inappropriately’ quashed. In the Dáil, Flanagan admitted he twice had penalty points cancelled, though he also asked that they be reinstated.

In June 2013, Flanagan came to prominence as an advocate of turf cutters whose ability to cut turf (peat) was affected by the European Union’s Habitats Directive. As part of his advocacy, Flanagan attended a number of turf cutters’ protests. Flanagan supports the cutting of turf from bogs including when they are protected as Special Areas of Conservation. Despite a European Union ban, he has cut turf at Cloonchambers Bog near Castlerea, a raised bog which has been designated a Special Area of Conservation.

On 21 March 2014, Flanagan announced that he would run as an independent candidate for the Midlands–North-West constituency at the 2014 European Parliament election. He ran on an “anti-European Union platform”. During the campaign he famously said, “I’m sick and tired of dealing with the monkey, I want to go and deal with the organ grinder.” He was elected on 26 May 2014, at the second count, after being deemed to have passed the quota.

In December 2014, Flanagan was named as having the second worst voting record among Irish MEPs at the European Parliament, as determined by VoteWatch Europe and reported in Ireland. He explained that this was as a result of his wife being ill and his children needing him.

He supported a ‘Yes’ vote in the 2018 Irish abortion referendum.

He was re-elected in the 2019 European Parliament election in May.

On 28 September 2020, a tweet was sent from Flanagan’s Twitter account at 2:50am which read, “Sapirse (sic) McHugh skinny dipping”, most likely a reference to Saoirse McHugh, a former member of the Green Party. Flanagan claimed the following day that he believed his Twitter account had been “compromised”.