Flores began his career in the youth ranks of Lima club Universitario de Deportes.

[2] With the national team, Flores participated at the 2018 FIFA World Cup and was the joint-top scorer (together with Paolo Guerrero) for Peru in the qualifiers for said competition, with five goals.

He made his official league debut in the Torneo Descentralizado on 31 July 2011 in an away match against Juan Aurich for matchday 16 of the 2011 season, at the age of 17.

Then in the 92nd minute of the derby, Flores dribbled past three Alianza Lima players and provide the pass that led to Martin Morel's winning goal.

In the 2016 season, he was a key part of an offensive quartet that also included Andy Polo, Raúl Ruidíaz and Diego Guastavino, which won the 2016 Torneo Apertura, after a 0–1 away victory against Sporting Cristal.

[16] In late August, Flores suffered a head-on-head collision and was out 6 weeks to repair facial fractures.

[21][22] One of the most iconic moments of his return, was his goal against Alianza Lima, to win the Peruvian championship for the first time in 10 years.

It eventually ended 1–1 and Chile qualified at the expense of Peru, but Flores' performance impressed then-manager Sergio Markarián and he was called to the senior squad for the first time in perpetration for the friendly against South Korea and the remaining matches of 2014 World Cup qualifying, but he only made his debut in the friendly against South Korea.

He left a great landmark in the team on his maiden major competition debut, scoring one goal against Ecuador in a 2–2 draw.

Although he didn't score other goal than the one he netted to Ecuador, he helped Peru to top the group and eliminated Brazil in process.

He scored the first goal against Chile in the semi-finals to send Peru into the finals against Brazil.On 21 December 2019, he married his long time girlfriend Ana Siucho in a televised wedding.