The stratospheric CO
2
oxygen isotope budget is thought to be governed primarily by the O(
1
D)+CO
2
isotope exchange reaction. However, there is increasing evidence that other important physical processes may be occurring that standard isotopic tools have been unable to identify. Measuring the distribution of the exceedingly rare CO
2
isotopologue
16
O
13
C
18
O, in concert with
18
O and
17
O abundances, provides sensitivities to these additional processes and, thus, is a valuable test of current models. We identify a large and unexpected meridional variation in stratospheric
16
O
13
C
18
O, observed as proportions in the polar vortex that are higher than in any naturally derived CO
2
sample to date. We show, through photochemical experiments, that lower
16
O
13
C
18
O proportions observed in the midlatitudes are determined primarily by the O(
1
D)+CO
2
isotope exchange reaction, which promotes a stochastic isotopologue distribution. In contrast, higher
16
O
13
C
18
O proportions in the polar vortex show correlations with long-lived stratospheric tracer and bulk isotope abundances opposite to those observed at midlatitudes and, thus, opposite to those easily explained by O(
1
D)+CO
2
. We believe the most plausible explanation for this meridional variation is either an unrecognized isotopic fractionation associated with the mesospheric photochemistry of CO
2
or temperature-dependent isotopic exchange on polar stratospheric clouds. Unraveling the ultimate source of stratospheric
16
O
13
C
18
O enrichments may impose additional isotopic constraints on biosphere–atmosphere carbon exchange, biosphere productivity, and their respective responses to climate change.