Long-term, episodic memory processing is supposed to involve the prefrontal cortex asymmetrically. Here we investigate the role of the dorsolateral prefrontal cortex (DLPFC) in encoding and retrieval of semantically related or unrelated word pairs. Subjects were required to perform a task consisting of two parts: a study phase (encoding), in which word pairs were presented, and a test phase (retrieval), during which stimuli previously presented had to be recognized among other stimuli. Consistently with our previous findings using pictures, repetitive transcranial magnetic stimulation (rTMS) had a significant impact on episodic memory. The performance was significantly disrupted when rTMS was applied to the left or right DLPFC during encoding, and to the right DLPFC in retrieval, but only for unrelated word pairs. These results indicate that the nature of the material to be remembered interacts with the encoding–retrieval DLPFC asymmetry; moreover, the crucial role of DLPFC is evident only for novel stimuli.