Season 2006–07 was a mixed season for Hibernian; their league form suffered from extended cup runs, and they eventually finished sixth. The reward for their cup form was a first trophy in 16 years, thrashing Kilmarnock 5–1 in the final to lift the CIS Cup. Hibs were knocked out of the Scottish Cup in a semi-final replay by Dunfermline.

The season was also notable for the departure of manager Tony Mowbray, the appointment of John Collins as his replacement and a players' revolt that quickly followed the CIS Cup triumph.

The competitive football started early in 2006–07 for Hibs due to their qualification for the Intertoto Cup. They were given a bye to the second round, where they comfortably beat their first opponents Dinaburg (Latvia) 8–0 on aggregate. Hibs were eliminated from European competition on the away goals rule by Danish team OB in the third and final Intertoto Cup round.

Hibs only played one friendly match in the 2006 pre-season, a 3–2 win at Easter Road against Premier League side Charlton Athletic.

Hibs got off to a slow start in the new league season, taking eleven points from the first nine matches. The highlight of the early part of the league season was a 2–1 win over Rangers on 17 September, but this was then followed with two disappointing losses against Falkirk and St Mirren, both by 1–0.

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