Single-cell analysis contributes to the understanding of cellular heterogeneity and behaviors. Nitric oxide (NO) is an important intracellular and intercellular signaling molecule, and the functions of NO are closely related to the balance between intra- and extracellular NO levels. In this manuscript, a convenient and reliable method based on a dual-labeling strategy using capillary electrophoresis (CE) separation with laser-induced fluorescence (LIF) detection has been presented for quantifying intra- and extracellular NO simultaneously in single cells. Followed by single-cell injection, a plug of HEPES buffer containing 1,3,5,7-tetramethyl-8-(3',4'-diaminophenyl)-difluoroboradiaza-s-indacene and disodium 2,6-disulfonate-1,3-dimethyl-5-hexadecyl-8-(3,4-diaminophenyl)-4,4'-difluoro-4-bora-3a,4a-diaza-s-indacene as the labeling reagents for intra- and extracellular NO, respectively, was aspirated from the inlet of the capillary. The on-line derivatization was carried out on the tip of the capillary at room temperature for 20 min. Then, the cell was lysed and NO derivatives were well separated within 14 min, producing mass detection limits (S/N = 3) of 2.4 and 8.1 amol for intra- and extracellular NO, respectively. The proposed method was validated by simultaneous analysis of intra- and extracellular NO in single macrophage cells. The dual labeling-based CE-LIF method holds great promise for research on the functions of NO as well as other bioactive molecules at the single-cell level.