Baguio started playing college ball at the University of Santo Tomas by suiting up for the school's basketball varsity squad, the Growling Tigers. When he arrived in Manila from Cebu in the summer of 1999, he initially tried out for La Salle. The Green Archers’ coaching staff was interested in adding him to their lineup with a condition that he would be spending time under Team B for a couple of years before he could move up. He was dismayed, so he decided to look for another school. The moment he tried out for Aric del Rosario, he knew he had found his new home in Manila. He joined the Tigers three years after UST won four straight UAAP Men’s Basketball championships. At the time he arrived, La Salle was the new league power. He was still a freshman when they met the Green Archers in the 1999 UAAP Finals where they defeated the Tigers for their second straight title. Citing academic deficiencies, he decided to sit out the entire 2001 season. Upon his return the following season, he led the Growling Tigers to the 2002 Final Four only to lose to the star-studded La Salle Green Archers squad. Nevertheless, he was selected as part of perhaps the deepest mythical five selection in the history of the UAAP that included University of the East's James Yap, Ateneo's Rich Alvarez and Enrico Villanueva and La Salle superstar Mike Cortez. He also suited up for Hapee/Kutitap Toothpaste in the PBL.
Professional career
He was drafted 14th overall by Red Bull in the 2003 PBA draft. Before the draft, many basketball pundits were expecting him to be a first round draftee because of his illustrious college career at UST. But during draft day, he was only picked in the second round, causing a shock to many basketball observers. During his rookie year, he played the support role but did well. Slowly, after Red Bull traded away its main men like Willie Miller, Kerby Raymundo, Lordy Tugade, Enrico Villanueva, and Mick Pennisi, he then emerged as the team's leading scorer and main skipper. He led his team in scoring and in other departments during his time with Red Bull. And on his last year with the team, he ended his stint still scorching the net by being among the top 10 leading scorers in the league, and by being an All-Star caliber player. During the latter part of the 2008–09 PBA season, he along with Red Bull teammate Celino Cruz were traded to the Air21 Express for 2011 and 2012 draft picks. This trade then led Yeng Guiao to resign as Red Bull coach. In 2008, he was named to the National Team under his former mentor in Red Bull, Coach Yeng Guiao. In 2009, unhappy with his tenure in Burger King, he was dealt to the Barangay Ginebra Kings. He became part of the talented backcourt of the Gin Kings, together with National Teammate Jayjay Helterbrand, Mark Caguioa and Ronald Tubid. He was also reunited with his 2003 batchmates, Enrico Villanueva, Sunday Salvacion, and Tubid. In the middle of the eliminations of the 2010 Fiesta Conference, Barangay Ginebra shipped Baguio via a blockbuster one-on-one trade to Alaska Aces for 2-time MVP Willer Miller. He considered this trade as the best thing that happened to his career. Since he was traded, he helped the Aces win the Fiesta Cup Finals and was awarded co-Finals MVP together with LA Tenorio. Three years later, he would win another championship in the 2013 PBA Commissioner's Cup at the expense of his former team, Barangay Ginebra. On July 31, 2014, he, together with JVee Casio and Sonny Thoss, signed new three-year contracts with the Aces, signalling his intention to remain with the Uytengsu franchise for the rest of his career. On July 13, 2016, he was traded along with 2017 2nd round pick to the Phoenix Fuel Masters for 2nd round picks in 2017 and 2018, respectively. On August 15, 2017, Phoenix traded him to the NLEX Road Warriors as a part of a three-team trade between the Fuel Masters, Road Warriors, and GlobalPort Batang Pier where he got reunited with Yeng Guiao.
