On 14 February 2009, Millar scored his first goal of the season in an Apertura tournament match that ended in a 2–0 victory over Universidad de Concepción at Estadio Monumental,where he scored the first goal of the game. On 22 April, he scored a goal in a Copa Libertadores match that ended in a 2–1 loss against Sport Recife in Brazil. He also scored the first goal at Colo-Colo's 5–2 win over Cobresal. At the end of season, Millar become the first footballer to contract swine flu on 16 June. He made a full recovery for the start of the Torneo Clausura.