When different stimuli indicate where and when to make an eye movement, the brain areas involved in oculomotor control must selectively plan an eye movement to the stimulus that encodes the target position and also encode the information available from the timing cue. This could pose a challenge to the oculomotor system since the representation of the timing stimulus location in one brain area might be interpreted by downstream neurons as a competing motor plan. Evidence from diverse sources has suggested that the supplementary eye fields (SEF) play an important role in behavioral timing, so we recorded single unit activity from SEF to characterize how target and timing cues are encoded in this region. Two monkeys performed a variant of the memory-guided saccade task, in which a timing stimulus was presented at a randomly chosen eccentric location. Many spatially tuned SEF neurons only encoded the location of the target and not the timing stimulus, while several other SEF neurons encoded the location of the timing stimulus and not the target. The SEF population therefore encoded the location of the each stimulus with largely distinct neuronal subpopulations. For comparison, we recorded a small population of lateral intraparietal (LIP) neurons in the same task. We found that most LIP neurons that encoded the location of the target also encoded the location of the timing stimulus after its presentation, but selectively encoded the intended eye movement plan in advance of saccade initiation. These results suggest that SEF, by conditionally encoding the location of instructional stimuli depending on their meaning, can help identify which movement plan represented in other oculomotor structures, such as LIP, should be selected for the next eye movement.