After the victory of Fianna Fáil at the 1997 election, Taoiseach Bertie Ahern appointed Martin to the Cabinet as Minister for Education and Science.

Weeks later, at the 2011 general election, Martin led Fianna Fáil to the worst result in its 85-year history, with a loss of 57 seats and a popular vote of just 17.4%.

At the 2016 general election, Fianna Fáil's performance improved significantly, more than doubling their representation in the Dáil: Martin continued to serve as Leader of the Opposition.

[17] Martin's time as a teacher was short-lived: he left after just one year to become a full-time politician, when he secured election to Cork Corporation as a Fianna Fáil candidate in 1985.

[20] When Fianna Fáil returned to power following the 1997 general election, Martin was appointed to the newly expanded position of Minister for Education and Science.

[29] In October 2003, Martin promised to examine cases of symphysiotomy in Irish hospitals which occurred during the 1940s and 1950s, and offered free health care to those affected.

[31] Letters containing death threats and shotgun cartridges, from a group calling itself the Irish Citizens Defence Force, were posted to Martin on 29 February 2008, at a prominent Dublin fertility clinic.

Martin and Cowen failed to convince the Irish public to support the ratification of the Treaty of Lisbon, and this protest expressed in the referendum on 12 June 2008 plunged the government into a major political crisis.

[37] While in Brussels on 22 February 2010, he questioned Foreign Affairs Minister of Israel Avigdor Lieberman over the use of fraudulent Irish passports in the assassination of Mahmoud al-Mabhouh.

He told Dáil Éireann that he had requested that the Israeli government allow the MV Rachel Corrie to deliver its cargo of aid to Gaza instead of involving itself in "further bloodshed".

[50] In September 2010, doubts about Brian Cowen's abilities and political judgment as Taoiseach and party leader emerged following a disastrous early-morning radio interview on Morning Ireland.

Cowen survived; however, that same month Martin admitted that he and other cabinet members, namely Brian Lenihan and Dermot Ahern, harboured ambitions to lead the party should a vacancy arise.

[51] While some backbench rebel Fianna Fáil TDs and senators called for Cowen to go, no cabinet minister publicly came forward to challenge the incumbent.

In spite of this, Martin once again expressed an interest in running for the leadership of Fianna Fáil once the vacancy arises in December 2010 on RTÉ's Saturday View radio programme.

[19] On 22 January 2011, just days after winning a vote of confidence, Brian Cowen announced that he was stepping down as leader of Fianna Fáil, but would remain as Taoiseach.

On a special RTÉ News programme that day, a number of Fianna Fáil TDs and senators came on the air and publicly backed Martin for the leadership.

[55] He was immediately seen as the front-runner; however, a number of other candidates, including Brian Lenihan Éamon Ó Cuív and Mary Hanafin, entered the field to ensure a contest.

[58] Martin led the party into the 2011 general election, which saw Fianna Fáil swept from power in the worst defeat of a sitting government in the history of the Irish state.

While Martin and other Fianna Fáil leaders concluded early on that they would not be re-elected to another term in government, they were surprised by the severity of the defeat; they had hoped to hold onto at least 30 seats.

[63] In an opinion poll in September 2011, Fianna Fáil's popularity fell to 10%, several points lower than its performance in the February 2011 election.

[68][69] Specifically, he said "he would vote in favour of repealing the Eighth Amendment and to allow abortion on request until near the end of the first trimester," leading to some political conflict within Fianna Fáil.

[74] In December 2018, Martin ruled out a 2019 general election, agreeing to a one-year extension between his party and Fine Gael in Ireland's "national interest".

[77] Cowen's successor Dara Calleary resigned that August following the Golfgate scandal, having attended a social hosted by the Oireachtas Golf Society which was contrary to national health guidelines surrounding the ongoing COVID-19 pandemic.

[79][80][81][82] Subsequently, there was much unrest within Fianna Fáil, with a number of TDs such as Jim O'Callaghan, Cathal Crowe, James Lawless and Marc MacSharry openly questioning in public whether or not Martin should lead the party into the next general election.

[92][93] In March 2024, Martin criticised the Israeli blockade of the Gaza Strip, saying that "The use of starvation as a weapon of war is a blatant violation of international humanitarian law.

[95] He was elected again as Taoiseach in a 95–76 vote by the Dáil on 23 January 2025 following a coalition agreement between Fianna Fáil, Fine Gael and with the support of several independent TDs.

[109] In 2021, Martin condemned legislation passed in Hungary which prohibited gay people from featuring in educational material, describing it as "unacceptable" and saying a strong response was needed from the European Union.

[110] In 2021, Martin expressed openness to changing laws regarding transgender teenagers and self-identification, stating he believed that "we should consult young trans people to hear their views".

[112] Martin, citing Jon Boutcher of Operation Kenova, Say Nothing by Patrick Radden Keefe, and Killing Thatcher by Rory Carroll says he believes the Troubles was a "futile war" in which the Provisional IRA did "more damage to their own people" than otherwise.

[114][115] Their seven-year-old daughter, Léana, died in October 2010 shortly before her eighth birthday at London's Great Ormond Street Hospital after suffering from a heart condition.