A warden was a chief administrative officer of a prison or penal colony - be they civilian or military in nature.
In the 2250s, feeling that he needed to pay for his crimes Alexander Simmons personally appealed to the warden of the New Zealand Penal Settlement to not be granted early release from custody. (DSC novel: Drastic Measures).
Commandant Koth served as the warden of the Klingon prison Rura Penthe in the 2290s. Koth was a participant in the Khitomer conspiracy. He attempted to kill James T. Kirk and Leonard McCoy in a manner that would not raise suspiscions, but the two Federation officers were rescued by the USS Enterprise before Koth could murder them. General Chang intended to have Koth killed for his failure, but died himself before he could have the execution carried out. (TOS movie: The Undiscovered Country).