Pahud attended the Conservatoire de Paris (Conservatoire National Supérieur de Musique de Paris) in France, studying with Michel Debost, Alain Marion, Pierre Artaud, and Christian Larde. Whilst studying, he won two major competitions, one in Duino 1988 and the other in Kobe in 1989. In 1988, Emmanuel also won the 2nd Prize at the International Scheveningen Music Competition in Scheveningen, Netherlands. Winning these competitions put Pahud in the forefront to become principal flautist in the Basel Radio Symphony, under the direction of Nello Santi which he obtained the position in 1989 whilst finishing his studies in Paris. He resigned from the orchestra in 1992. Pahud also held the principal flautist position at the Munich Philharmonic under Sergiu Celibidache. Pahud graduated at the age of 20 from the Conservatoire in 1990, obtaining the First Prize (Premier Prix). He then continued to advance his studies for the next two years; in style and interpretation with one of France’s greatest flautists, Swiss-born Aurèle Nicolet who turned out to be his neighbor.
Pahud at 22 was the youngest player in the Berlin Philharmonic, a position to which he returned in 2002 under Sir Simon Rattle after taking a 18 month sabbatical in 2000 in order to teach the Virtuosity Class at the Conservatoire de Musique de Genève for one year and to perform in concerts worldwide. In 2007, Pahud was voted onto the Media Vorstand (or the Member of the Media Board) of the BPO. He currently shares the position of Principal Flautist with Andreas Blau who has held the position since 1969.
Pahud has appeared as soloist with internationally renowned orchestras in addition to the Berlin Philharmonic: the Yomiuri Nippon Symphony Orchestra, the London Symphony Orchestra, the Tonhalle Orchester Zurich, L’Orchestre de la Suisse Romande, the Berlin Radio Symphony Orchestra (East Berlin), and the Danish Radio Symphony also known as the Danish National Symphony Orchestra. He also appears regularly at leading festivals throughout Europe, the United States and the Far East. His more famous international concerto appearances and collaborations of the past few seasons (2005–2008) included the Berlin Philharmonic, the Baltimore Symphony Orchestra, the London Philharmonic Orchestra, the Monte-Carlo Philharmonic Orchestra, the Bavarian Radio Symphony Orchestra, the NHK Symphony Orchestra, the Berliner Barock-Solisten, the Vienna Radio Symphony Orchestra, the Orchestre National de Belgique, the Orchestre Philharmonique de Radio France and a U.S. tour with the Barcelona Symphony and Catalonia National Orchestra (including a Carnegie Hall debut).
In March 2008 Pahud performed the World Premiere of another work commissioned by Frank Michael Beyer, who composed Meridian, a Concerto for Flute & String Ensemble. Other World Premieres include the Flute Concerto by Luca Lombardi in 2010 and Concerto for Flute & Ensemble by Elliot Carter, which Pahud premiered in September 2008 in Jerusalem. In 1996 he signed an exclusive contract with EMI Classics, the only flutist in the world to have a solo recording contract with a major record company.