On May 24th 2004, Mowbray was surprisingly appointed manager of Hibernian, replacing Bobby Williamson. He gained much acclaim for the job he has done, winning the SPL manager of the year award in his first season. Hibs finished in the top four in the SPL in his only two full seasons in charge. This marked the first time in three decades that Hibs had finished in the top four places of the top division in consecutive seasons.
Hibs progressed to the later stages of every domestic cup competition in his tenure, and made two appearances in European football, losing to Dnipro Dnipropetrovsk in the 2005/06 Uefa Cup, and losing on the away goals rule to OB Odense in 2006/07 Intertoto Cup.
Tony Mowbray improved Hibernian into a team consistently challenging at the top end of the Scottish League for the first time in three decades. During his tenure, season ticket sales at Easter Road almost doubled.