Different theories have been proposed to explain how the human brain derives an accurate sense of time. One specific class of theories, intrinsic clock theories, postulate that temporal information of a stimulus is represented much like other features such as color and location, bound together to form a coherent percept. Here, we explored to what extent this holds for temporal information after it has been perceived and is held in working memory for subsequent comparison. We recorded EEG of participants who were asked to time stimuli at lateral positions of the screen followed by comparison stimuli presented in the center. Using well-established markers of working memory maintenance, we investigated whether the usage of temporal information evoked neural signatures that were indicative of the location where the stimuli had been presented, both during maintenance and during comparison. Behavior and neural measures including the contralateral delay activity, lateralized alpha suppression, and decoding analyses through time all supported the same conclusion: The representation of location was strongly involved during perception of temporal information, but when temporal information was to be used for comparison, it no longer showed a relation to spatial information. These results support a model where the initial perception of a stimulus involves intrinsic computations, but that this information is subsequently translated to a stimulus-independent format to be used to further guide behavior.