With the help of former Anorthosis Famagusta player and Latvian international Marians Pahars Júnior was taken on trial at Skonto Riga in July 2008. He signed a four-year contract as the trial was successful. Right after joining Júnior found it difficult to fit into the squad, as there were many experienced players, and was soon loaned out to Olimps/RFS. He played 15 matches that season and was mainly used in the right-back position. In December 2008 Júnior returned to Skonto Riga and was mainly used as a late game substitute by that time club's manager Paul Ashworth. In 2009 Skonto had a lack of forwards as two of them left right before the start of the season, and Júnior was tried out as a forward. He scored twice on his new position debut against Jūrmala-VV, and later on remained in that position. He played 19 games and scored 5 goals in the 2009 season, and was notified as a forward in the squad for the 2010 season. He made a big surprise in the upcoming season, scoring 18 goals in 24 league matches and sharing the top-scorer's honour with Liepājas Metalurgs striker Deniss Rakels, who had also netted 18 times respectively. In 2010 Skonto became the champions of Latvia. After the impressive season Júnior went on trials with Maccabi Haifa in Israel, Dynamo Moscow in Russia and Energie Cottbus in Germany, but didn't settle there. At the start of 2011 season Júnior suffered an injury and didn't appear in the first league matches of the season. Despite lack of gaming practice, he showed his ability right after being declared fit, and soon became the leading scorer of the league yet again. He was named the league's best player in July 2011. Although, Skonto had a poor season and finished only in the 4th place of the Latvian Higher League, Júnior became the league's top scorer with 22 goals in 26 games. After the season, he was included in the LFF and sportacentrs.com teams of the tournament and was also named the best forward of the season.
After seven months without club, Nathan signed with Paços Ferreira on 31 January 2019 after a trial.
International career
Nathan Júnior has not represented Brazil at any level yet. In an interview for sportacentrs.com the player admitted that he would be interested in representing Latvia, but as the Latvian law does not allow more than one citizenship, Júnior would have to waive the Brazilian passport and play in Latvia for at least five years. The player said that it would be a serious decision, but after moving to Austria this question has been put aside.
