Purpose <p>To investigate the correlation between endometrial preparation protocols, embryonic development stages, and ectopic pregnancy.</p> Methods <p>A total of 29,700 clinical pregnancies, all of which resulted from freeze–thaw cycles performed between January 2018 and December 2023, were analyzed in this retrospective study.</p> Results <p>The ectopic pregnancy rate was significantly higher in artificial cycles than natural cycles (1.5% vs. 0.8%; <i>P</i> &lt; 0.001); the ectopic pregnancy rate was significantly higher in stage 5–6 than stage 3–4 blastocyst transfer (1.3% vs. 0.7%; <i>P</i> = 0.019). After incorporating all independent confounders into a multivariate general estimating equation model, artificial versus natural cycle (adjusted RR = 1.68, 95% CI = 1.32–2.13; <i>P</i> &lt; 0.001) was shown to be an increased risk factor for ectopic pregnancy, especially in the single embryo transfer subgroup (aRR = 1.75, 95% CI = 1.23–2.48; <i>P</i> = 0.002); additionally, day 3 embryo transfer versus blastocyst transfer (aRR = 1.97, 95% CI = 1.15–3.38; <i>P</i> = 0.014) and stage 5–6 blastocyst versus stage 3–4 blastocyst transfer (aRR = 1.70, 95% CI = 1.05–2.74; <i>P</i> = 0.031) were shown to be increased risk factors for ectopic pregnancy.</p> Conclusions <p>This study found that endometrial preparation protocols and embryonic development stages are significantly associated with ectopic pregnancy.</p>