The 20-year-old had started the season brightly and forced his way into the first-team reckoning after a 17-goal campaign last year to help the club's reserve side – Sevilla Atletico – earn promotion to the second tier.
Fernandez, a Sevilla youth product, also scored his first LaLiga goal in the dying stages of its 2-1 win over Las Palmas on 11 September, before enjoying a positive second-half cameo 11 days later against bitter rival Real Betis.
However, after initial treatments on a knee injury suffered in training had no effect, Sevilla has acknowledged that surgery is the only way forward and he looks set for a lengthy lay-off.
An official club statement read: "Carlos Fernandez will definitely undergo surgery in order to overcome the knee injury he suffered on October 6 in training.
"Conservative treatment which he has undergone since then has not taken effect and, after being reviewed today by Dr. Cugat in Barcelona, it has been determined that surgical intervention is definitely needed to solve the partial tear of the anterior cruciate ligament in his left knee.
"This type of injury requires six to eight months for recovery. It seems unlikely Carlos can return to action this season."