Objectives This study aimed to characterize the patterns of medication use before, during and after pregnancy in a population-based cohort of women with systemic lupus erythematosus (SLE). Methods Using population-based administrative data in British Columbia, Canada, with valid information on start date of pregnancy, we identified women with SLE who had singleton pregnancies ending in deliveries between January 1, 2002, and December 31, 2012. We assessed the proportion of SLE pregnancies exposed to SLE medications – namely antimalarials and immunosuppressants – as well as glucocorticosteroids, and nonsteroidal anti-inflammatory drugs (NSAIDs) 24 months before pregnancy, each trimester of pregnancy, and 12 months postpregnancy. We also assessed discontinuation of antimalarials and immunosuppressants, defined as no prescriptions in a given window following a prescription in a preceding window. Results Of 376 pregnancies (284 women) with SLE, 24.2% had one or more dispensing for antimalarials, 8.2% for azathioprine, 19.7% for glucocorticosteroids and 4.8% for NSAIDs during pregnancy. We observed a 16.7% discontinuation of antimalarials in the year prior to pregnancy, 29.8% in the first trimester, 9.7% in the second trimester, and 26.0% in the third trimester. We also observed a 29.2% discontinuation of azathioprine in the first trimester, 8.0% in the second trimester, and 9.1% in the third trimester. Conclusions These population-based data show frequent discontinuation of medications, particularly antimalarials, in SLE pregnancies. These findings suggest the importance of educating women with SLE who are pregnant or planning to become pregnant on the benefits and risks of medications during pregnancy.