Nitrous oxide (N2O) is an important greenhouse gas and the major source of stratospheric reactive nitrogen (NOy), an active participant in the stratospheric chemistry controlling ozone depletion. Tropospheric N2O abundances are increasing at nearly 0.3% yr−1 and this increase is expected to continue in the near future as are direct stratospheric NOy perturbations, for example, from aircraft. In order to test and gain confidence in three-dimensional (3-D) model simulations of the stratospheric N2O-NOy system, a simplified photochemistry for N2O and NOy is developed for use in chemistry transport models (CTMs). This chemical model allows for extensive CTM simulations focusing on uncertainties in chemistry and transport. We compare 3-D model simulations with measurements and evaluate the effect on N2O and NOy of potential errors in model transport, in column and local ozone, and in stratospheric temperatures. For example, with the three different 3-D wind fields used here, modeled N2O lifetimes vary from 173 to 115 years, and the unrealistically long lifetimes produce clear errors in equatorial N2O profiles. The impact of Antarctic denitrification and an in situ atmospheric N2O source are also evaluated. The modeled N2O and NOy distributions are obviously sensitive to model transport, particularly the strength of tropical upwelling in the stratosphere. Midlatitude, lower-stratospheric NO2/N2O correlations, including seasonal amplitudes, are well reproduced by the standard model when denitrification is included. These correlations are sensitive to changes in stratospheric chemistry but relatively insensitive to model transport. The lower stratospheric NOy/N2O correlation slope gives the correct net NOy production of about 0.5 Tg N yr−1 (i.e., the cross-tropopause flux as in the Plumb-Ko relation) only when N2O values from 250 to 310 ppb are used. As a consequence, the Synoz calibration of the flux of O3 from the stratosphere to the troposphere needs to be corrected to 550±140 Tg O3 yr−1.