In August 2013, Emenike moved back to Turkey by returning to Fenerbahçe for a fee worth around €13m (£10.2M). He was noted to be "thrilled" and was quoted saying Fenerbahce had always been a dream for him, and he had returned to perform for the fans and win championships. His first match for Fenerbahçe against Torku Konyaspor ended in a 3–2 loss. He scored his first goal for Fenerbahçe in October 2013 against Kayserispor in the 94th minute, securing a last minute win. He scored two more against Gaziantepspor a week later, while Fenerbahçe won 3–1.
Emenike was called up to the Nigeria national football team for a friendly against Sierra Leone. He was called up to Nigeria's 23-man squad for the Africa Cup of Nations. On 21 January 2013, he scored in Nigeria's opening AFCON match against Burkina Faso in a 1–1 draw. He also scored the first goal in the quarter final match between Nigeria and Côte d'Ivoire which Nigeria won 2–1. On 3 February, Emenike scored a 30-yard free kick giving his country a 2–1 win over Côte d'Ivoire in the African Cup of Nations.
In 2013, he became part of the third Nigerian team to win the African Cup of Nations – Nigeria's first continental victory since 1994. His four goals proved crucial to Nigeria's progress through the tournament, and he was named to the team of the African Cup of Nations Team of the Tournament. However, Emenike wasn't included in the final, due to a thigh injury. He also received the Pepsi Tournament Top Scorer, with four goals, along with Ghana's Wakaso Mubarak.
In March 2013, Emenike was left out of the Nigerian squad for the World Cup qualifier, due to hamstring injury, which Emenike criticised Nigeria's coach and officials of ignoring him. In June 2013, Emenike wasn't included for Nigeria's squad at the 2013 FIFA Confederations Cup. After four month without being called up, Emenike was called up for August's Mandela Cup friendly match but did not participate due to injury. Emenike celebrated his absence from Eagles in Sept 2013 when he played in the 2014 world cup qualifier against Malawi – played in Calabar. He scored a goal in the two-nil win by the Super Eagles – a win which took them to the final round of world cup qualifiers. He came on as a substitute three days later in a friendly match against Burkina Faso, played in Kaduna – he scored the fourth goal in a 4–1 win for the Eagles.
On 13 October 2013, in the first-leg of last round of the World Cup qualifier against Ethiopia, he scored twice to give the Super Eagles a 2–1 lead going into the second-leg On 20 October 2015 he announced his retirement.