Nausea and vomiting of pregnancy (NVP) is a common condition reported however inconclusively among pregnancies after assisted conception. The study objective was thus to explore whether NVP is associated to mode of conception or other in vitro fertilization (IVF)-related variables. This nested matched cohort study, originating from the BASIC-project, was conducted at the Uppsala University Hospital in Sweden between 2010 and 2016. IVF pregnancies (n = 210) and age and parity-matched women with spontaneous pregnancies (n = 420) comprised the study sample. The study outcome was self-reported NVP at gestational week 17. IVF treatment and pregnancy data were obtained after scrutinization of the medical records. NVP with or without medications was not associated with mode of conception (chi-square test, p = 0.889), even after adjusting for potential confounders. In a subgroup analysis among IVF pregnancies, NVP without medication was more frequently seen in the group who received cleavage stage embryos vs blastocysts (chi-square test, p = 0.019), exhibiting a marginally significant but strongly increased effect even after adjustment [crude RRR 3.82 (95% CI 1.23–11.92) and adjusted RRR 3.42 (95% CI 0.96–12.11)]. No difference in the rate of NVP with or without medication between women that underwent fresh and frozen/thawed embryo transfers as well as IVF or ICSI was observed. Conception through IVF is not associated with NVP. Transfer of a blastocyst may decrease the risk of developing NVP and further, large-scale prospective studies are required to validate this finding.