Baclao attended high school and the first few years of college at the West Negros University, where he led the WNU Mustangs to the 2005 National University Games (Unigames) crown in Bacolod City and the 2006 Basketball Association of the Philippines (BAP) National Students Championship (Inter-Collegiate) title. His reputation as a major defensive contributor, especially in blocking and rebounding, was noticed by Manila-based college scouts, and in 2006 he was recruited by Ateneo de Manila University, which was led by Japeth Aguilar and Chris Tiu among others.
After serving the mandatory one-year residency rule imposed by the University Athletic Association of the Philippines, Baclao made it to the Blue Eagles roster in the 2007 UAAP season, where he contributed to the team's defense, although they failed to make it to the Finals. In 2008, he was designated as the team's co-captain, which he held until his last year of eligibility. In those last two seasons, Baclao averaged 6.1 points per game, 5.9 rebounds per game, and 1.9 blocks per game. He played a major role in the Blue Eagles' conquest of their archrivals, the De La SalleGreen Archers in the 2008 UAAP Basketball championships. He was adjudged as the Finals MVP and the Smart Defensive Player of the Year.
In his final UAAP season, where Baclao shared the captaincy with Jai Reyes and Rabeh Al-Hussaini, he averaged 6.4 points per game, 8.4 rebounds per game, 2.5 blocks per game, and 1.4 assists per game in 27.9 minutes per game, and was a key factor in the Eagles' defense of the UAAP title against the University of the EastRed Warriors.
Weeks after leading the Eagles to its second straight UAAP basketball championship, Baclao signed with the Philippine Patriots, the country's professional team playing for the ASEAN Basketball League. Coach Louie Alas saw him reprising his role he had with the Blue Eagles as he backstopped the team's defense. To date, Baclao's superb clutch plays off the bench has helped the Patriots win games, especially their rematch against the Singapore Slingers in Manila on November 7, 2009, where they won, 70-53.
He became the top pick of the 2011 PBA Draft, a draft class that featured fellow Blue Eagle Rabeh Al-Hussaini, Letran swingman Rey Guevarra and Sean Anthony. He immediately made impact with his first team providing solid defense. However, his performance was not as stellar as that of Al-Hussaini. Still, he was awarded as a member of the All-Rookie Team by season's end. On his second year, his minutes went down and was seldom used by the Boosters. During the 2012 off-season, he, along with Niño Canaleta, Robert Reyes and John Wilson were traded to the Air21 Express. Under Franz Pumaren, his play became better and is now among the regularly used players on the team. He was again traded on October 13, 2013 in a three-team trade that involved Air21, Talk 'N Text, and Meralco.  On September 22, 2014 Baclao and Harold Arboleda were traded to GlobalPort for Jay Washington. This trade is a part of a multiple team trade between GlobalPort, Talk 'N Text, and NLEX.