Peter Pekarik commenced his professional club football career at FK ZTS Dubnica in 2004 and played for them for one season. He then moved to MSK Zilina and played for them for three seasons, scoring 5 goals in 111 league appearances. He won the Corgon Liga with them in 2007.
Pekarik was signed by Wolfsburg in 2009 and featured in 16 matches for the German champions of 2008-2009.
Peter Pekarik made his international debut for Slovakia in 2006 and has featured in over 10 international matches for his nation.