The west African country also dropped to the seventh place in Africa.
Nigeria were on the 47th spot and sixth position respectively in the FIFA rankings and continental football in April and May.
An official statement on FIFA's website on Thursday said the recent flurry of pre-FIFA World Cup friendlies left its mark on the latest rankings.
Nigeria's Super Eagles were beaten 1-0 by the Czech Republic on Wednesday, during a last pre-World Cup friendly played in Austria.
Last Saturday, the team also saw a defeat by the Three Lions of England. The match, played at the Wembley Stadium, ended 2-1.
Nigeria had played a 1-1 draw on home soil against DR Congo on May 28.
Nigeria's World Cup opponents Argentina, Croatia, and Iceland are on fifth, 20th and 22nd positions respectively in the FIFA rankings.
Nigeria will face Croatia on June 16 at the football's greatest showcase.