In the mid-1990s, Uichico had a coaching stint with the Green Archers and guided them to two runner-up trophies. He also joined the Magnolia Beverage Masterscoaching staff during Norman Black and Jacobs tenure. In 1999, Uichico became the new head coach of the Beermen after Jacobs' departure. After an early elimination in the All-Filipino Cup, he coached the Beermen to the Commissioner and Governors Cup titles during the 1999 campaign, ending San Miguel's five-year title drought. He is also the first rookie coach to lead his team to back-to-back titles in the same year, a feat duplicated by Siot Tanquingcen in 2005. In 2000, Uichico once again guided San Miguel to two more titles and laid claim to his first and only Coach of the Year plum. His first All-Filipino Cup title with the Beermen came in 2001, defeating sister team Barangay Ginebra Kings. Ron Jacobs appointed Uichico as one of his assistants for the RP team's 2002 Asian Games campaign. However, after Jacobs suffered a stroke, Uichico was named as the new head coach of the national squad. Uichico guided the Philippines to a fourth-place finish in the event. Their semifinal loss against eventual tournament winner South Korea was a crushing blow for Uichico's squad losing by one point on a Lee Sang Min triple in the final seconds. Despite the loss, the team still brought home what is known to Filipino basketball fans as "The Silent Gold." He returned as San Miguel's head coach after the Asian Games campaign, but went on a four-year title drought before winning his sixth PBA title in six years in the 2005 Fiesta Conference. The Beermen defeated the Talk 'N Text Phone Pals 4-1.
On August 3, 2006, Chot Reyes was named as the new head coach of the San Miguel Beermen replacing Uichico. and the, San Miguel Corporation moved Uichico to San Miguel's sister team the Barangay Ginebra Kings replacing Siot Tanquingcen, who was demoted as one of Uichico's assistants. On his first Ginebra coaching stint, he was able to win a championship in the 2006–07 PBA Philippine Cup that season. A year later, he won his 2nd championship with the Gin Kings in the 2008 PBA Fiesta Conference and his 8th overall title. In 2012, he left Ginebra to coach the Smart Gilas National Team.
Uichico will lead the Philippinenational team that will participate at the 2017 Southeast Asian Games instead of the Chot Reyes, who will be leading the Philippine squad which will compete at the 2017 FIBA Asia Cup due to an overlapping schedule between the two competitions.
