[5] On February 20, 2019, he made his professional and New York Red Bulls debut coming on in the 74th minute for Alex Muyl in 2–0 victory in a 2019 CONCACAF Champions League fixture at Atlético Pantoja.
On March 2, 2019, Fernandez made his league debut with the club, appearing as a starter in a 1–1 draw with Columbus Crew on the opening day of the season.
[6] On March 12, 2019, Omir scored his first professional goal in a 4–2 defeat to Mexican side Santos Laguna in a CONCACAF Champions League match in Torreon, Mexico.
[11] On February 26, 2022, Fernandez scored the winning goal for New York in a 3–1 victory over San Jose Earthquakes in the opening match of the season.
[13] On May 9, 2023, Fernandez scored the lone goal for New York in 1–0 victory over rival DC United, helping his side advance to the Round of 16 of the 2023 U.S. Open Cup.