Red Bull Barako (2005–2007) Before entering the PBA, Fonacier continued to rehab from his ACL injury, and took master's classes in communications. He was then selected by
Red Bull Barako with the 14th pick. In his rookie season, Fonacier helped Red Bull win a
Fiesta Conference championship. He won the
PBA Rookie of the Year award during the
2005–06 season. This made him the lowest picked player in PBA history to win the award, until Aaron Black broke the record. In a 92–89 loss to the
Air21 Express during the
2006–07 season, Fonacier had a chance to make a game-winning play, but his pass was stolen by
Yancy de Ocampo. During that time, he was named as an All-Star, and played for the North All-Stars team in the
2007 PBA All-Star Weekend. He also participated in that year's Three-Point Shootout.
Magnolia Beverage Masters (2007–2008) Fonacier was then traded to the
Magnolia Beverage Masters. There, he split time with
Lordy Tugade,
Chris Calaguio, and former Ateneo teammate Wesley Gonzales on a team that was in "win-now" mode. Alaska made it to the
finals, where in Game 5, he recorded 15 points and six rebounds. However, they lost their next two games, and the
Talk 'N Text Tropang Texters became champions.
TNT Franchise (2010–2017) 2010–11 season During the
2010 PBA Draft, he was traded by the Aces to the
Talk 'N Text Tropang Texters in exchange for the draft rights of
Elmer Espiritu. This was done because Talk 'N Text had just traded away
Mac Cardona. He was able to contribute as Talk 'N Text won the
2010–11 Philippine Cup. He then had clutch free throws in a win over the
Meralco Bolts during the
2011 Commissioner's Cup. The Tropang Texters won the
Commissioner's Cup finals in six games. During the
Governors' Cup, he had a career-high 27 points on 8-of-11 shooting from three in a win over the
Powerade Tigers. For that performance, he won Player of the Week. The Texters topped the elimination round, but lost to the
Petron Blaze Boosters in seven games in the
finals.
2011–12 season In the Game 1 of their
Philippine Cup semis against Petron, Fonacier scored half of his 22 points in the fourth quarter, and made two clutch free throws to secure the win. From there, they lost their next three games and went down 3–1, but they overcame that deficit and defeated Petron. He won the Mr. Quality Minutes award that season for his valuable contributions off the bench and leading the team in minutes played.
2012–13 season Talk 'N Text started the
2012–13 season 4–0, with them getting their fourth win by Fonacier scoring 18 of his 26 points in the first half and hitting clutch shots in the fourth to go along with seven rebounds against the
San Mig Coffee Mixers. They got their fifth straight win with him scoring seven of his 12 points in the fourth quarter against the
Rain or Shine Elasto Painters. Their streak ended at the hands of Alaska when he missed a shot that could have sent that game into overtime. Against
Barangay Ginebra, he had 16 points, but fouled out of the game as Ginebra managed to hang on for the win. The Texters made it to the semifinals against Alaska where in Game 3, he had 21 points after not making any three pointers in the first two games. They managed to beat Alaska to return to the
finals. From there, they swept Rain or Shine in four games. This championship was sweeter for Fonacier, as this was Coach
Norman Black's first conference with TNT, and he was able to share this championship with multiple coaches from his time at Ateneo. He then went on a shooting slump in his next nine games as he averaged 4.4 points on 22% shooting from the field. He also played in the All-Star Game during the
2013 All-Star Weekend as a member of
Gilas Pilipinas. After his stint with Gilas, he returned for the
2013 Governors' Cup, in which he had 19 points in a win over the
Globalport Batang Pier. They didn't qualify for the playoffs that conference, as they lost to Ginebra in the eighth seed playoff.
2013–14 season In the
2014 Commissioner's Cup, Fonacier had 16 points with four three-pointers in a win over the
Barako Bull Energy as Talk 'N Text started the conference with four straight wins. He followed that up with 14 points in a win over Meralco. Heading into the All-Star break, the Texters were 7–0.
2014–15 season In the
2014–15 Philippine Cup, Fonacier had 11 points with back to back threes at the end of the third quarter in a win over Barako. In a close
Commissioner's Cup game against NLEX in which they were up by one with eight seconds remaining, he called a timeout even though the team didn't have one. NLEX import
Al Thornton tied the game on a technical free throw, but Fonacier's teammate
Jayson Castro won the game for Talk 'N Text with a pull-up jumper. Talk 'N Text won the Commissioner's Cup title that season. In the
Governors' Cup, he scored a season-high 20 points in a win over the
Blackwater Elite.
2015–16 season During the offseason, Fonacier re-signed a three-year deal to stay with Talk 'N Text for three more years. The Texters got their first win of the season when he contributed 11 points against the
Mahindra Enforcer. He then had 16 in a win over Blackwater. In the
2016 Commissioner's Cup, he missed a game against NLEX due to sickness. They lost to Alaska in a best-of-three quarterfinal series in that conference, despite 19 points from him in Game 3. They then started the
Governors' Cup with six straight wins, but lost to Mahindra despite 13 points from him in that game. In a win over Globalport, he had 14 points and a crucial offensive rebound that allowed
Ranidel de Ocampo to make the game-winning shot for TNT. He then had a season-high 21 points in 32 minutes off the bench to go along with seven rebounds, two assists, and a steal as they increased their record to 9–1. TNT made it to the semifinals against Meralco where in Game 3, he had 20 points, but Meralco took the series lead 2–1. They lost the next game, and Meralco moved on to the
Governors' Cup finals.
2016–17 season In a
2016–17 Philippine Cup game, Fonacier had 15 points as they got their first win of the season over Ginebra. He then had 16 points on four triples along with four boards, one assist, and one steal in 28 minutes in a win over Alaska. With a new head coach in
Nash Racela, he enjoyed a career resurgence as in their first five games of the conference, he averaged 10.8 points built around 2.2 triples, three rebounds, 1.4 assists, and 0.8 steal in 27.3 minutes. TNT finished the elimination round with a record of 6–5. In Game 1 of their quarterfinals series against Globalport, he had 17 points and went five of nine from distance. They moved on to the semis against the
San MIguel Beermen, where in a Game 4 loss, he had a team-high 15 points. However, he was given a rare technical foul for 'disrespectfully addressing the referee' just when the team was at the height of a fourth quarter rally. He led the team with 14 points in a Game 7 loss, and the Beermen moved on to the
finals. Fonacier also competed once again in the Three-Point Shootout during the
2017 All-Star Week. In his final game with TNT, he had 14 points on 5-of-10 shooting, with four of his shots coming from beyond-the-arc.
NLEX Road Warriors (2017–2022) 2016–17 season In a four-team trade, Fonacier went from playing for TNT to playing for the
NLEX Road Warriors. TNT gained
Anthony Semerad and a first round pick from Globalport. With NLEX, he reunited with his former head coach from Red Bull, Coach Guiao, and assumed the role of a veteran for the young NLEX team. He didn't play for NLEX in the
2017 Commissioner's Cup, as he had undergone surgery for bone spurs and with NLEX not in the playoffs, had no need to rush his recovery. In the
2017 Governors' Cup, he had 12 points in a win over Ginebra. He then had 16 points, seven boards, two assists, two steals, and only one turnover in 30 minutes in an upset win over Meralco. NLEX then clinched a spot in the quarterfinals with a 103–100 win over SMB as he logged 16 points, four rebounds, three assists, two blocks, and one steal in 29 minutes. He stepped up in the clutch, as he made two clutch triples, inbounded the ball that led to free throws for
JR Quiñahan, and blocked
Alex Cabagnot's attempt to send the game into overtime. With his performance in that game, he earned a PBA Press Corps Player of the Week citation. In the quarterfinals, they lost to the
Star Hotshots.
2017–18 season During the
2017–18 Philippine Cup, Fonacier had 12 points, including a four-point play that gave NLEX a four-point lead that eventually led to the win over the
Kia Picanto. He had 12 again in a Christmas Day win over Globalport. They had their first loss of the season against the
Phoenix Fuel Masters despite him scoring a team-high 22 points. NLEX lost three more games after that, but they were able to stop the losing streak with a win over Ginebra in which he produced 17 points on 7-of-12 shooting. Then he contributed 17 points, six rebounds, and one block while also going 4-of-4 from three as
Kiefer Ravena made the game-winning jumper over the Bolts. In a win over the Aces, he,
Kevin Alas, and
Raul Soyud combined for 45 points. They faced Alaska again in the quarterfinals where in Game 1, he had 18 points and nine rebounds. From there, they moved on to the semifinals where they lost to the Hotshots in five games. In the
2018 Commissioner's Cup, Fonacier had an all-around performance of 12 points, seven boards, and six assists in a win over the
Columbian Dyip. He also competed once again in the Three-Point Shootout during the
2018 All-Star Week. He then had 14 points in a loss to his former team TNT. He was then ruled out for the rest of the Commissioner's Cup after a collision in mid-air with Ginebra's
Jervy Cruz led to a bruised rib and a collapsed lung. Fonacier made his return in the first game of the
Governors' Cup against TNT. In that game, he had 17 points and the win, making 50% of his 10 shots from the field. In NLEX's first three games, he had led NLEX to a 2–1 record despite the absence of Coach Guiao, multiple injured players, and him not at full strength. He then led the team to another win, this time over the Dyip. In NLEX's win over Blackwater, Coach Guiao returned, NLEX snapped Blackwater's four-game winning streak, and he scored 24 points on 8-of-13 shooting. He then led NLEX with 21 points in losses to Ginebra and Meralco. That conference, they lost to Ginebra in the first round.
2019–2022: Final seasons with NLEX In the
2019 season, Fonacier played in less games. This was mostly due to an injury. On April 4, 2019, he was reactivated. He scored seven points in a loss to the Batang Pier. In 2020, Fonacier didn't join the team in the PBA bubble as his wife had health issues. He still attended team meetings and workouts and also assisted the coaching staff. Fonacier rejoined NLEX the following year. He skipped the
2021 Philippine Cup for personal reasons. He was then assigned to NLEX's 3x3 team, the
Cavitex Braves. In 2022, Fonacier was reactivated by NLEX at the start of the
2022–23 PBA season. In his final conference, he played in seven games and averaged 1.2 points as the Road Warriors didn't make the playoffs. His contract expired on December 31, 2022, and he did not renew his contract. == National team career ==