The measurement of the time difference between two heterogeneous electrical sources is a necessary task in several branches of metrology. In particular the dissemination of Coordinated Universal Time (UTC) around the world requires one to quantify the synchronization between two or more co-located time scales. The task is usually carried out using a time interval counter, by directly measuring the time difference between signals at its inputs. We found that special care must be taken when a total uncertainty significantly smaller than 1 ns is desired. The goal of this paper is to present a complete analysis of the total uncertainty for the measurement of time differences between co-located time scales, with considerations for improvement.