The day after leaving CSSD in 1987, Nesbitt got a bit part in Virtuoso, a BBC Two Screen Two television play about the life of John Ogdon. He worked for two days on the play, earning £250 per day. His first professional stage appearance came in the same year, when he played Keith in Up on the Roof. The musical ran at the Theatre Royal, Plymouth, before transferring to the London West End. Nesbitt reprised the role when the production returned to Plymouth in early 1989. Roger Malone in The Stage and Television Today wrote that Nesbitt "steals the show with the best lines and best delivery as he laconically squares up to life with an easy contentment". Nesbitt appeared in two other plays in 1989; in June, he played Dukes Frederick and Senior in Paul Jepson's As You Like It at the Rose Theatre Club, and then appeared in Yuri Lyubimov's version of Hamlet. Hamlet had been translated back to English from Boris Pasternak's Russian translation. It ran at the Haymarket Theatre, Leicester for a month before a transfer to the Old Vic and then a nine-month world tour. Nesbitt played Guildenstern, Barnardo and the second gravedigger. He recalled that the play received "shocking" reviews, but was exciting.

In the early 1990s, he lived with fellow actor Jerome Flynn and earned money by signing fan mail for the successful star of Soldier Soldier. In his debut feature film, Hear My Song (Peter Chelsom, 1991), Nesbitt played Fintan O'Donnell, a struggling theatrical agent and friend of Mickey O'Neill (Adrian Dunbar). A New York Times critic wrote, "the jaunty, bemused Mr. Nesbitt, manages to combine soulfulness with sly humor". The praise he received made him self-assured and complacent; in 2001, he recalled, "When I did Hear My Song, I disappeared so far up my own arse afterwards. I thought, 'Oh, that's it, I've cracked it.' And I'm glad that happened, because you then find out how expendable actors are." His attitude left him out of work for six months after the film was released. Until 1994, he mixed his stage roles with supporting roles on television in episodes of Boon, The Young Indiana Jones Chronicles, Covington Cross, Lovejoy, and Between the Lines. In 1993, he appeared in Love Lies Bleeding, an instalment of the BBC anthology series Screenplay and his first appearance in a production directed by Michael Winterbottom; he later appeared in Go Now (1995), Jude (1996) and Welcome to Sarajevo (1997). A Guardian journalist wrote that "he showed himself to be a generous supporting actor" in Jude and Sarajevo.

Back on stage, he appeared as Doalty in Translations (Gwenda Hughes, Birmingham Repertory Theatre, 1991), Aidan in Una Pooka (Mark Lambert and Nicolas Kent, Tricycle Theatre, 1992), Damien in Paddywack (Michael Latimer), Cockpit Theatre, 1994), and Jesus in Darwin's Flood (Simon Stokes, Bush Theatre, 1994). Paddywack, in which Nesbitt's character is suspected by others of being an IRA member, transferred to the United States for a run at the Long Wharf Theatre in New Haven, Connecticut in October 1994. A Variety critic called Damien "the play's only fully developed character" and commended Nesbitt for giving "the one strong, telling performance [of the cast]". In 1996, Nesbitt appeared in an episode of the BBC Northern Ireland television drama Ballykissangel, playing Leo McGarvey, the ex-boyfriend of Assumpta Fitzgerald (Dervla Kirwan) and love rival of Peter Clifford (Stephen Tompkinson). He reprised the role for four episodes in 1998.

In 1996, Nesbitt auditioned to play Adam Williams, the male lead in Cold Feet, an ITV Comedy Premiere about three couples in different stages of their romantic relationships. The audition came about through a mutual friend of Nesbitt's and the director, Declan Lowney. The producer, Christine Langan, had also recalled his performances in Hear My Song and Go Now. Adam had not been written with an Irishman in mind to play him—English writer Mike Bullen had written the character as a thinly veiled portrayal of himself in his youth—but Nesbitt wanted to take the opportunity to appear in a contemporary drama as an ordinary man from Northern Ireland with no connection to the Troubles, especially after the Troubles-based plot of Love Lies Bleeding. Cold Feet was a critical success; it won the 1997 Golden Rose of Montreux and the 1997 British Comedy Award for Best ITV Comedy and was thus commissioned for a full series. Cold Feet's first series aired at the end of 1998 and was followed by the second series in 1999. A storyline in that series featured Adam being diagnosed with testicular cancer, which inspired Nesbitt to become a patron of the charity Action Cancer.

By the time of the third series, Nesbitt and the other cast members were able to influence the show's production; an episode featuring Adam's stag weekend was due to be filmed on location in Dublin but Nesbitt suggested it be filmed in Belfast and Portrush instead. Several scenes were filmed at his old workplace Barry's Amusements, although they were cut from the broadcast episode. At the end of the fourth series in 2001, Nesbitt decided to resign and move on to other projects. Executive producer Andy Harries persuaded him to stay for one more series by suggesting that Adam be killed off, so Nesbitt signed on for the fifth series. During pre-production of the fifth series, Mike Bullen decided to kill off Adam's wife Rachel (played by Helen Baxendale) instead.

Cold Feet ran for five years from 1998 to 2003, and Nesbitt won the British Comedy Award for Best TV Comedy Actor in 2000, the Television and Radio Industries Club Award for Drama TV Performer of the Year in 2002, the National Television Award for Most Popular Comedy Performance in 2003, and the TV Quick Award for Best Actor in 2003. Nesbitt credits the role with raising his profile with the public. Further television roles during these five years included women's football team coach John Dolan in the first two series of Kay Mellor's Playing the Field (appearing alongside his Cold Feet co-star John Thomson), investigative journalists Ryan and David Laney in Resurrection Man (Marc Evans, 1998) and Touching Evil II respectively, and womaniser Stanley in Women Talking Dirty (Coky Giedroyc, 1999).

Nesbitt's performance in Hear My Song had also impressed first-time screenwriter and film director Kirk Jones, who cast him in his 1998 feature film Waking Ned. Playing amiable pig farmer "Pig" Finn brought Nesbitt to international attention, particularly in the United States (where the film was released as Waking Ned Devine); the cast was nominated for the 1999 Screen Actors Guild Award for Outstanding Performance by a Cast in a Theatrical Motion Picture. In 1999, he appeared as the paramilitary "Mad Dog" Billy Wilson in The Most Fertile Man in Ireland (Dudi Appleton). The following year, he appeared in Declan Lowney's feature debut, Wild About Harry. Lowney had personally asked him to appear in the supporting role of cross-dressing Unionist politician Walter Adair. In 2001, he made his debut as a lead actor in a featur…

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Nesbitt had been approached at a British Academy Television Awards ceremony by director Paul Greengrass, who wanted him to star in a television drama he was making about the 1972 "Bloody Sunday" shootings in Derry. Nesbitt was only seven years old when the shootings happened and was ignorant of its cause; he believed that there was "no smoke without fire" and that the Catholic marchers must have done something to provoke the British Army. He was filming Cold Feet in Manchester when he received the script. He read it and found that had "an extraordinary effect" on him. Nesbitt played Ivan Cooper in Bloody Sunday, the man who pressed for the march to go ahead. To prepare for the role, Nesbitt met with Cooper and spent many hours talking to him about his motives on that day. He met with relatives of the victims and watched the televised Bloody Sunday Inquiry with them, and also read Don Mullan's Eyewitness Bloody Sunday and Peter Pringle and Philip Jacobson's Those Are Real Bullets, Aren't They?. Greengrass compared Nesbitt's preparation to an athlete preparing for a race, and told The Observer, "For an Irish actor, doing the Troubles is like doing Lear." Nesbitt had questioned whether he was a good enough actor to effectively portray Cooper and was worried what Derry Catholics would think of a Protestant playing the lead, although Ivan Cooper himself is a Protestant.

Shortly before Bloody Sunday was broadcast, Nesbitt described it as "difficult but extraordinary" and "emotionally draining". The broadcast on ITV in January 2002 and its promotion did not pass without incident; he was criticised by Unionists for saying that Protestants in Northern Ireland felt "a collective guilt" over the killings. His parents' home was also vandalised and he received death threats. During the awards season, Nesbitt won the British Independent Film Award for Best Performance by an Actor in a British Independent Film and was nominated for the British Academy Television Award for Best Actor. The film was also screened at film festivals such as the Stockholm International Film Festival, where Nesbitt was presented with the Best Actor award.

In an analysis of the film in the History & Memory journal, Aileen Blaney wrote that it is Nesbitt's real-life household name status that made his portrayal of Cooper such a success. She reasoned that Nesbitt's celebrity status mirrors that of Cooper's in the 1970s: "A household name across Great Britain, Northern Ireland and the Irish Republic [sic], Nesbitt's widespread popular appeal is emphatically not contingent upon his Protestant Ulster identity, and consequently the double-voicing of the character he plays does not alienate viewers of an alternative, or no, sectarian persuasion." Guardian journalist Susie Steiner suggested that his appearance in Bloody Sunday was an attempt to resolve the expression of his "Irishness" on screen: "Where he has taken part in a sectarian theme, his intelligence as an actor has often been masked by an excessive, cartoon-style comedy. Yet in his more successful, high-profile roles, (notably in Cold Feet, and as Pig Finn in the gently pastoral film Waking Ned), Nesbitt's Irishness has been exploited for its romantic charm. It has been sugared and, in the process, de-politicised." A critic identified Bloody Sunday as Nesbitt's "coming of age" film, and Nesbitt called it a turning point in his career. He refers to his career since the film was released as "post-Bloody Sunday".