Objectives To evaluate knowledge, attitude and perception of community pharmacists towards pharmacogenomics services. Methods A cross-sectional study was conducted among community pharmacists in two cities in Northern Nigeria using a self-administered, validated and pre-tested questionnaire. The data were collected from December 2021 to February 2022 and were analysed using both descriptive and inferential analyses. Results A total of 161 completed questionnaires were included in this study (response rate was 61.9%). Most of the respondents were males (59.0%). Only 25.5% had previous pharmacogenomics training but 90.1% indicated an interest in attending pharmacogenomics training in the future. Overall, respondents had moderate knowledge of pharmacogenomics with higher knowledge score found among those who had previous pharmacogenomics training (11.9 ± 1.7 vs 10.5 ± 2.4; p = 0.001), and those with postgraduate qualification (11.7 ± 1.9 vs 10.7 ± 2.3; p = 0.028). The mean attitude score was 6.8 ± 2.0 out of 10.0 indicating a good attitude towards pharmacogenomics services. Those with previous training (8.1 ± 1.7 vs 6.2 ± 1.9; p < 0.001) and those with postgraduate qualification (7.2 ± 2.3 vs 6.6 ± 1.9; p = 0.042) had better attitude towards pharmacogenomics services. The median perception score was 34.0 out of 45.0, indicating a positive perception towards pharmacogenomics. There was a better perception among those with previous pharmacogenomics training (40.0 [21–45] vs 34.0 [0–45]; p = 0.002) and those with postgraduate qualifications (39.0 [0–45] vs 34.0 [21–45]; p = 0.010). Barriers to the implementation of pharmacogenomics included lack of knowledge (89.4%), lack of guidelines (87.5%) and lack of reimbursement (81.4%). Conclusion Community pharmacists have a moderate knowledge, a good attitude and a positive perception towards pharmacogenomics services. Those with previous pharmacogenomics training and those with postgraduate qualifications had better knowledge, attitude and perception towards pharmacogenomics services. Lack of knowledge, lack of guidelines and lack of reimbursement were the major barriers to the implementation of pharmacogenomics services in community pharmacies in Nigeria. Pharmacogenomics should be included in pharmacy training curricula to prepare pharmacists for the provision of pharmacogenomics services. Development of local guidelines and a robust reimbursement plan for pharmacogenomics services is recommended.