Brown played junior football in the Fife Youth League with clubs including Inverkeithing United and Foulford Royals of Cowdenbeath. He signed for Hibernian professionally in 2002 and made his debut as a substitute in a 3-1 win over Aberdeen in May 2003. He made his first starting appearance the following week, a 1-0 win over Motherwell. He started in Hibs’ remaining two matches of the season and scored in both, a double in a 2-1 against Livingston and in a 3-2 defeat to Partick Thistle.
The following season (2003-04) he became a regular fixture in the Hibernian team, playing 41 times in all competitions and netting 4 goals. Despite a disappointing league campaign, in which they eventually finished 8th, Hibs reached the final of the League Cup, defeating both Celtic and Rangers en route. However, they were defeated 2-0 by Livingston in the final. Brown featured in all the matches of Hibs’ League Cup run and scored in the 9-0 win over Montrose in the third round.
In season 2004-05, Brown, along with several other young players at the club, flourished under the guidance of new manager Tony Mowbray. Brown, largely due to missing four months of the season due to an injury sustained against Celtic, only featured 23 times for Hibs, scoring twice, including the second goal in a 3-1 win over Celtic at Celtic Park.
Season 2005-06 was also blighted somewhat by injury. He missed most of the second half of the season due to a broken leg and missed Hibs’ Scottish Cup semi-final against Hearts. He did, however, feature in the final Edinburgh derby of the season, coming on as a substitute as Hibs won 2-1.
Brown handed in a transfer request to the Hibernian assistant manager, Tommy Craig, directly after their home game against Dundee United on 2 December 2006. The action was thought to be taken on the advice of Brown’s agent Willie McKay.
On 31 January 2007, however, Brown announced that he was retracting his transfer request and was now ‘happy’ to remain with Hibernian for the duration of his contract (which was due to end in summer 2009). Despite this, media rumours continued to suggest that he would move to Rangers in summer 2007. Former Hibernian teammate Kevin Thomson, who signed for Rangers in January 2007, claimed to have spoken with Brown about joining him at Rangers. Subsequent reports linked him with a transfer to other clubs in the summer, including Celtic, Everton, Tottenham Hotspur, Middlesbrough and Reading. Reading confirmed that they reached agreement with Hibernian to sign Brown but the player said “If I had chosen Reading I would probably be fighting a relegation battle next season and then maybe disappearing into the Championship. In two years’ time people would have been saying, ‘Remember that lad Scott Brown – whatever happened to him?'”.
Despite intense speculation about his future, Brown helped Hibs win their first trophy in 16 years as they won the League Cup, defeating Kilmarnock 5-1 in the final.
He scored in his final appearance for Hibs against future employers Celtic, on 20 May 2007 at Easter Road, a match in which the Hibees won 2-1. The goal was celebrated by both the Hibs and Celtic supporters, he was also given a standing ovation from both sets of fans when he was taken off late on.