Henrique played his youth football in Brazil with América Mineiro and in 2003 joined Dutch giants Feyenoord. After failing to break into the first team, Henrique returned to Brazil where he played senior football with América and was loaned out to several other Brazilian clubs. Henrique is nicknamed the Slippery Fish.
Henrique joined Brisbane Roar initially as a temporary injury replacement for fellow Brazilian Reinaldo in February 2009, after impressing coach Frank Farina in a week-long trial after being given permission to talk with the Australian club by América.
He made his first appearance as a second-half substitute in the Roar's second-leg 2–1 win over Central Coast Mariners in the 2009 A-League semi-finals. There was minor controversy due to the transfer being completed only four hours before his debut appearance. Henrique signed a one-year contract with the Roar on 4 March 2009, after impressing during his loan spell.
On 17 September 2009, he signed a new three-year deal with the Roar. Henrique missed up to two months of the 2010–11 season because of a broken arm, which he injured in a match against Melbourne Victory, courtesy of Kevin Muscat. Henrique came back as a wild card for the Roar and in the 2010–11 grand final against Central Coast Mariners, scored a goal in extra-time and the winning penalty.
On 4 May 2014, Henrique scored the winning goal against the Western Sydney Wanderers in the 2014 Hyundai A-League Grand Final at Suncorp Stadium.
On 14 November 2014, Henrique came off the bench and scored a hat-trick as Brisbane Roar registered their first win of the season with a 4–0 result over Newcastle. Henrique finished the season rather early, as he was required to undergo knee reconstruction, effectively ruling him out for the rest of 2014–15. Despite this, he finished 2014–15 as his most successful, netting eight goals in 16 games.
Henrique netted a stunning goal, his third of the season, from half-way, lengthwise equivalent to 45 metres, as Roar defeated Melbourne City 3–1.
On 16 June 2016, it was announced that Henrique would depart the Roar after seven seasons with the club.
On 27 August 2016, Henrique joined Adelaide United on a one-year deal. On 4 December 2016, Henrique scored a brace against Wellington Phoenix to win Adelaide United's first match of the 16/17 season, as the match ended 2–0.
On 31 January 2017, Henrique left Adelaide United after 13 games to join Thai club Chiangrai UnitedBrisbane Roar
A-League Premiership: 2010–11, 2013–14
A-League Championship: 2010–11, 2011–12, 2013–14