Vertical profiles of nitrous oxide (N<sub>2</sub>O) and its isotopocules, isotopically substituted molecules, were obtained over the equator at altitudes of 16–30 km. Whole air samples were collected using newly developed balloon-borne compact cryogenic samplers over the Eastern Equatorial Pacific in 2012 and Biak Island, Indonesia in 2015. They were examined in the laboratory using gas chromatography and mass spectrometry. The mixing ratio and isotopocule ratios of N<sub>2</sub>O in the equatorial stratosphere showed a weaker vertical gradient than the previously reported profiles in the subtropical and mid-latitude and high-latitude stratosphere. From the relation between the mixing ratio and isotopocule ratios, further distinct characteristics were found over the equator: (1) Observed isotopocule enrichment factors (<i>ϵ</i> values) in the middle stratosphere (25–30 km) are almost equal to <i>ϵ</i> values reported from broadband photolysis experiments conducted in the laboratory. (2) <i>ϵ</i> values in the lower stratosphere (< ca. 25 km) are about half of the experimentally obtained values, being slightly larger than those observed in the mid-latitude and high-latitude lower stratosphere. These results suggest the following. (1) The time scale of horizontal mixing in the tropical middle stratosphere is sufficiently large for in-situ photolysis of N<sub>2</sub>O, mainly because of strong upwelling and transport barrier between the tropics and extratropics. (2) The air in the tropical lower stratosphere is exchanged with extratropical air on a time scale that is shorter than that of photochemical decomposition of N<sub>2</sub>O. Previously observed <i>ϵ</i> values, which are invariably smaller than those of photolysis, can be explained qualitatively using a three-dimensional chemical transport model and using a simple model that assumes mixing of <q>aged</q> tropical air and extratropical air during residual circulation. Results show that isotopocule ratios are useful to examine the stratospheric transport scheme deduced from tracer–tracer relations.