San Rafael Zelaya started his career playing for
San Rafael in 2004, where he played for one year. The following season, he moved to Atlético La Merced. In July 2006, both Zelaya and Rúsvel Saravia were offered contracts to play for one of El Salvadors biggest clubs,
Águila. Unfortunately for both Zelaya and Saravia, they could not come to terms with the club over their proposed salaries, and as a result, the transfer fell through.
Intipucá Zelaya then moved on to play in
Segunda División with
Intipucá. After 2 years with the club, Zelaya caught the attention of
Chalatenango coach
Vladan Vićević.
Chalatenango After meeting with Vićević, Zelaya was offered, and accepted a contract to play with his first
Primera División club Chalatenango. Zelaya went on to impress in his
first season with the club and grew a fan base with both spectators and reporters for being one of
El Salvador's most promising young strikers. Chalatenango finished in fifth place in the league table with 25 points. Zelaya scored 8 goals at the end of the Clausura 2008.
Alianza In 2008, Zelaya moved to
Alianza after former Chalatenango president Lisandro Pohl switched clubs. This switch lead to Pohl taking various players with him to
Alianza whose rights he supposedly owned due to them being bought when he was president at Chalatenango.
Mexico On 15 June 2009, Zelaya was one of the three Salvadoran footballers signed to Mexican club
León on a loan deal, the other two were
Cristian Castillo and
Julio Enrique Martínez. On 3 December 2009, it was announced that
Club León had permanently signed Zelaya along with the other two Salvadorans with a three-year contract. On 12 December 2009, it was confirmed by Alianza's own president, Lisandro Pohl, that Zelaya would return to
Alianza on a loan deal. Zelaya later played without a loan deal and participated at the
Clausura 2011, where he was top goalscorer with 13 goals to his part. He also had the opportunity to reign champion and score 2 goals at the final to give his team the tournament.
Russia On 19 July 2011, Zelaya signed with
Russian First Division club
Alania Vladikavkaz on a loan transfer for six months. Alania may be able to redeem his transfer by January 2012. On 9 August 2011, Zelaya debuted at the
Russian league championship in a match against
Torpedo Vladimir as a starter. On 4 November, he scored two goals against
Mordovia Saransk, but also received a knee injury that would rule him out for 7 months. During the summer of 2012, Alania decided not to keep him and sent him back to
Alianza. On 26 January 2013, he once again signed a six-month loan to rejoin Alania Vladikavkaz, who had been promoted to the
Russian Premiere League. He was sent back to
Alianza in June after his contract expired.
Return to Alianza In June 2014, Zelaya signed again with Alianza. Zelaya scored four goals in a 7–0 victory against Chalatenango in the second leg of the quarterfinals of the Apertura 2018, at the
Estadio Cuscatlán, in December 2018. Alianza reached the semi-finals.
Los Angeles FC On 30 January 2019, it was announced that Zelaya would join
Major League Soccer club
Los Angeles FC. In January 2020, the club announced that it and Zelaya had mutually agreed to part ways.
Las Vegas Lights (loan) On 15 August 2019, Zelaya was loaned to
USL Championship side
Las Vegas Lights FC.
Retirement On January 24, 2025 a day after Alianza announced the mutual parting ways, Zelaya announced he would retire from professional football. He will be leaving as Alianza F.C. all time goal scorer with 176 goals in 385 games, he holds the club record most goal in a final series with 32 goals, hold the club record most individual goalscoring titles with 5 and won 8 club titles. ==International career==