Yotún first began by playing at the age of 7 in the youth academy Academia Deportiva Cantolao until the age of 12. Then he joined the youth divisions of Circolo Sportivo Italiano for two seasons. Then the following years he was in the youth divisions of Deportivo Real FC, alongside Manuel Tejada. In 2007, he transferred to one of Peru’s largest clubs, Sporting Cristal, and played in their youth team.

In January 2008 he was loaned out to José Gálvez FBC for the 2008 Descentralizado season. There Yotún made his professional debut on 5 March 2008 in the Torneo Descentralizado in an away league match against Coronel Bolognesi FC. He entered the match in the 46th minute for Renzo Guevara, and the match finished in a 1–1 draw. Yotún scored his first official goal on 9 March 2008 in a league match at home against Atlético Minero, which resulted in 1–0 win for his club. He played his last game for José Gálvez FBC on 14 December 2008 in the last fixture of the season, which finished in a 2–2 draw at home against Universidad San Martin. He made a total of 28 league appearances and scored 3 goals in his first season in the Descentralizado. This contributed to his club José Gálvez avoiding relegation that season by finishing in 9th place, just 5 points above the relegation zone.

In January 2009 Yotún returned to Sporting Cristal for the 2009 Descentralizado season. He made his official debut for Sporting Cristal on 9 May 2009 in a league match at home against FBC Melgar. Making his debut at the San Martín de Porres Stadium, he entered the match in the 46th minute replacing Yancarlo Casas, and the match finished in a 2–1 win for Melgar.

In 2011, Yotun’s impressive performances for Sporting Cristal convinced the new Peru national team coach Sergio Markarian to call him up for the 2011 edition of Kirin Cup. Against Japan, he made his national team debut substituting Jesus Rabanal in the 62nd minute. Though on 9 September 2013 against Uruguay for the fight for 5th place in the CONMEBOL World Cup Qualification group, Yotun’s performance was heavily criticized by Peruvians because of his expulsion during the game, which many argued had cost Peru’s qualification into the tournament.

Yotún played his 100th Descentralizado match for Cristal on 27 May 2012 in Round 15 away to Juan Aurich. He was also handed the captain’s armband after Carlos Lobaton’s red card in the 61st minute, but his side could not score the equaliser as the match finished in a 1–0 win for Aurich.

On 27 January 2015 Swedish champions Malmö FF announced that they had signed Yotún on a three-year contract. He arrived in Malmö as a left back, where he played for the 2015 season. After becoming the third choice left back behind newly arrived Behrang Safari and Pa Konate during the 2016 season, Yotún was played at various midfield positions, where he excelled. Yotún emerged as a key player during the first half of the 2017 season, and was voted Malmö FF player of the month by the supporters in July.

In 2015, Yotun was part of the team that finished 3rd in Copa América. He also featured in all three group games of the 2016 Centenario edition but was suspended on yellow card accumulation for Peru’s quarter-finals loss to Colombia.

Yotún signed for Orlando City of Major League Soccer on 4 August 2017 He made his debut on August 13 in a 3-1 defeat to New York Red Bulls. On September 28, Yotún scored his first goal for Orlando in a 6-1 win over New England Revolution, a game in which he also registered two assists. Despite his brief spell in MLS, Yotún was selected as an All-Star in 2018.

On December 27, 2018, Yotún was sold to Cruz Azul of Liga MX for $4 million.