Abstract Genetic counseling and genetic testing are essential for individuals with congenital heart disease/defects (CHD/CHDs). However, the clinical practices of genetic counselors (GCs) and their preferences for different CHD genetic testing strategies are previously unexplored. To address these gaps, GCs ( n  = 112) representing diverse specialties completed an online survey regarding their counseling and testing practices for syndromic CHD and apparently isolated/non‐syndromic CHDs (iCHD). We found practice variability around family screening recommendations, with prenatal respondents reporting lower prevalence of this practice for iCHDs ( p  = 0.0004). We found that all specialties considered chromosomal microarray (CMA) the most common prioritized genetic test for syndromic and iCHD, while more prenatal respondents considered FISH and karyotype useful for iCHDs compared to postnatal respondents ( p  = 0.0002 and p  = 0.002, respectively). Among postnatal respondents, a higher proportion considered exome/genome sequencing as useful compared to prenatal respondents ( p  = 0.0159); specifically, postnatal respondents' preference for exome/genome sequencing for iCHDs was ~2.6‐fold higher than prenatal respondents. We estimated participants' assessment of utility for different genetic testing modalities for iCHDs and found that prenatal respondents assigned higher mean utility to FISH ( p  = 0.0002), karyotype ( p  = 0.0006), and CMA ( p  < 0.0001). There were relatively moderate to decreased utility scores for gene panels and exome/genome sequencing for iCHDs compared to cytogenetic testing, across all specialties. Overall, these results provide insight into GC practices and use of various genetic testing strategies for syndromic CHDs and iCHDs. Findings may help inform and/or standardize clinical practices for CHD genetic testing, though additional studies are warranted.