Having joined Portuguese first division powerhouse FC Porto in 1996, Hilário found opportunities hard to come by and served several loan stints in the country. In three seasons (the first still on loan) with Madeira's Nacional, he developed as a topflight goalkeeper.

Hilário joined Chelsea on 1 July 2006 from Nacional, joining former Porto boss José Mourinho, the two having coincided there for a brief period, in the 2003–04 pre-season. He was originally signed as third-choice goalkeeper, as backup to Petr Čech and Carlo Cudicini, but was handed a run in the first team after both Čech and Cudicini sustained injuries in Chelsea's game against Reading on 14 October 2006. Hilário made his Chelsea debut on 18 October 18, against Barcelona at Stamford Bridge, keeping a clean sheet in a 1–0 win. He made his league debut three days later, against Portsmouth.

Hilário's run in the side saw him make a total of 18 appearances during the 2006–07 season and keep eight clean sheets; he also saved a penalty in an away game against Sheffield United. Čech's return to fitness in February 2007 saw him relegated to the substitute's bench again, and he was an unused replacement in Chelsea's League Cup final win over Arsenal. On the 2006–07 Chelsea season review DVD bonus features, there was a segment titled "Top Ten Saves of the Season." Several of the saves were Hilário's.

At the start of the 2007–08 season, Hilário found himself again third-choice to both Čech and Cudicini, but made a substitute appearance against Blackburn Rovers at Ewood Park, after the Czech suffered a hip injury. He then went on to start against Newcastle United and Fulham, as Chelsea won both contests 2–1. On 8 April 2008, he made a substitute appearance against Fenerbahce, due to injury to Cudicini, in the second leg of the quarter-finals of the UEFA Champions League, and kept a clean sheet. Portuguese newspapers subsequently hinted at a possible call-up to the Portuguese national side.

On 26 January 2009, Cudicini left Chelsea for Tottenham Hotspur, leaving the Portuguese as second-choice, and promoting reserve keeper Rhys Taylor to first team. On 7 February, Hilário made his first 2008–09 start after an injury to Čech, against Hull City, and kept a clean sheet in a 0–0 draw. Hilário was an unused substitute during Chelsea's 2009 FA Cup Final win over Everton.

On 26 September 2009, when Čech was red carded against Wigan Athletic after a tackle on Hugo Rodallega he came on for Florent Malouda and let in two goals, one which was a penalty. Due to Čech's suspension, Hilário was in the starting lineup for the game against Liverpool at Stamford Bridge on 4 October 2009. Besides performing well against Liverpool, he also kept a clean sheet and went on to receive the Barclays Man of the Match award.