He started his career playing in the Costa Rican Second Division with Santos de Guápiles and then he moved to AD Guanacasteca. Then in 2001, Cartaginés decided to bring him to the top division. He debuted on September 16 of that year against Pérez Zeledón and soon became a valuable player for this team, helping them to stay at the top division with his great saves. By the end of the 2003-2004 season, Alajuelense decided to loan Ricardo González to the Guatemalan club Comunicaciones so they asked Cartaginés to have him loaned. He debuted with his new team on April 25 of 2004 and became usual at the starting line-up soon after he got to the team. By the end of this season Alajuelense decided to purchase him and he went on to play 154 league games for Liga.
In 2010, Alfaro rejoined his first club Santos and in 2012 he returned to Cartaginés. Besides football, he owns an inflatable games rental company in El Tejar de El Guarco where he lives.
In December 2014, Alfaro retired and was named goalkeeper coach at Alajuelense.