Šokota joined Porto from rivals S.L. Benfica, where he played between 2001 and 2005. He previously played four seasons for Croatian First League side Dinamo Zagreb, who signed him to his first professional contract from his youth club NK Samobor in 1997. While playing for Dinamo Zagreb, he became the top goalscorer of the Croatian First League in both 1999-2000 and 2000-01 seasons, scoring 21 and 20 goals respectively. He also made several appearances in the UEFA Champions League with the club during their participations in the 1998 and 1999 group stages of the competition.
Šokota debuted for the Croatian national team in their second-leg Euro 2004 qualifying play-off match versus Slovenia in November 2003 and also played all three matches at the Euro 2004 finals in Portugal before the Croatian team exited the competition in the group stage. He won a total of eight caps and scored two goals for Croatia, netting one goal apiece in 2004 friendlies versus Turkey and Denmark, but was no longer called up to play for the team following the Euro 2004 finals.
By the end of 2004, and after refusing all Benfica's contract renewal proposals, Šokota was relegated to Benfica B, the club's reserve squad, where he eventually played for the rest of the 2004-05 season. On 25 January 2004, he played in a 1 - 0 away win against Vitória de Guimarães, a game overshadowed by the tragic death of his team mate Miklós Fehér. In June 2005, after his contract with Benfica finally expired, he joined rivals FC Porto on a free transfer. He has been plagued by injuries in his time in Portugal, having undergone four major surgeries. While at FC Porto, his first injury was in the beginning of the 2005-06 season, and he only returned to an official match on the last day of the Portuguese league. Soon, in the 2006-07 pre-season, he had another injury and as a result he played his first Superliga match against C.F. Estrela da Amadora on February 3, 2007
Šokota returned to his hometown club Dinamo Zagreb in March 2007.
In July 2009 Šokota moved to the Belgian League, signing a contract with Lokeren.
In August 2010 he went on loan to Olimpija Ljubljana for the 2010-2011 season.