The cued task-switching paradigm is often used to study cognitive control. In this paradigm, people are generally slower and make more errors when switching tasks as compared with repeating the same task. When two cues are mapped to each task, these switch costs could result from a mixture of cue-switch effects (which are thought to reflect cue encoding) and task-switch effects (which are thought to reflect task set preparation). In the behavioral literature, there has been a lively debate on the degree to which cue-switch effects and task-switch effects indeed reflect different phenomena. In the present study, we used fMRI to examine whether and to what extent the neural network underlying task-switch effects is also involved in cue-switch effects. We found task-switch but no cue-switch effects in the frequently observed preparation-related activation in fronto-parietal areas. These results suggest that the fronto-parietal areas displaying preparatory activity in task-switching paradigms are engaged in task preparation but not in cue encoding and that task preparation and cue encoding rely on completely different processes.