Since 1999, Botero was a regular player for the Bolivia national team, including participations in the 1999 FIFA Confederations Cup, in which he played in all three of Bolivia's group stage matches, the 2001 Copa América and the 2004 Copa América. On 1 April 2009, Botero scored a hat-trick for Bolivia in a historic 6–1 victory over Argentina in a 2010 FIFA World Cup qualifier, Argentina's first loss under the recently appointed manager, Diego Maradona. On 15 May 2009, Botero surprisingly announced the end of his era with the national team, putting as an excuse that his motivation "was not there anymore." In his ten years playing for Bolivia, Botero earned a total of 48 caps and scored 20 goals, becoming the highest scorer in the national team's history, before being surpassed by Marcelo Moreno in 2020. He represented his country in 30 FIFA World Cup qualification matches, scoring 16 goals.