The 36-year-old Spanish international missed the start of the season with injury and he made his ISL debut on October 18 in a 0-1 home loss to Delhi Dynamos.
The club said Marchena has left the club due to personal reasons.
"Unfortunate, Carlos Marchena has gone back to Spain due some personal reason, and will not be with for the rest of the season. We thank him for his time here and wish him the best. We are in talks with James McFadden as possible new international signing," Kerala Blasters CEO Viren D'silva said in a release.
Kerala beat FC Pune City in their first win in seven matches today and they are now at seventh spot in the eight-team ISL table with eight points from eight matches.