Background: The decision of whether to prescribe antidepressants (AD) and anxiolytics (AX) to pregnant women is complex, with serious potential ramifications. Clinicians’ perception of the risk of teratogenicity significantly influences their prescribing decisions and in turn impacts maternal decision making. Our cross-sectional study sought to discern differences in perceived risk between Obstetricians and Gynaecologists (O&Gs) and General Practitioners (GPs) when prescribing these medications in pregnancy. Furthermore, we investigated factors impacting perception, clinicians’ willingness to prescribe and their approach to provision of patient information. Methods: This cross-sectional study was conducted via a nation-wide online SurveyMonkey extended to Royal Australian and New Zealand College of Obstetricians and Gynaecologists (RANZCOG) database-derived affiliates: GP diplomates, fellows and trainees (5409 survey invitations: 545 respondents). O&Gs and GPs were compared using Pearson Chi-squared test for categorical variables and the Student t-test for continuous variables. Results: GPs reported higher rates of being aware of up-to-date medication prescription recommendations (57.6%) compared with O&Gs (44.2%). GPs also reported higher rates of training adequacy in psychotropic prescription (56.1% versus 29.0%). There was evidence to suggest GPs level of confidence in knowledge base, initiation and prescription of AD and AX was higher than those of O&Gs. The mean perception of patient non-compliance was similar between clinician groups (approximately 35%), but GPs perceived the extent of patient anxiety as higher compared to O&Gs (mean 73.7% (SD 21.3) versus 63.1% (SD 24.1), p<0.001). Both groups showed a strong preference for improved training rather than patient-focused technology (above 70% for both groups). Conclusion: Further development of clinician training in perinatal psychotropic prescription is warranted.