Limited information is available regarding the population structure of extra-intestinal pathogenic Escherichia coli (ExPEC) in Africa. Antimicrobial resistance profiles, sequence types (STs) and fimH types were determined on 60 clinical ExPEC from Nigeria using a 7-single nucleotide polymorphism quantitative PCR and sequencing of certain genes. Different ST131 clades were identified with a multiplex PCR. The isolates were mostly obtained from urines (58.3%). Not-susceptibility rates were as follows: trimethoprim-sulfamethoxazole (98%), cefotaxime (68%), gentamicin (55%), ciprofloxacin (62%) and piperacillin-tazobactam (2%). Dominant STs were associated with CTX-M-15 and included ST131-fimH30 (23%), ST457-fimH145 (20%), ST405-fimH27 (13%) and ST95-fimH41 (10%). We found the 7-SNP qPCR to be simple and cost-effective that can be utilized to tract different ExPEC clones on a global scale. This study provided insight into the population structure of ExPEC from Nigeria showing high prevalence of the rarely reported ST457 and the presence of multidrug resistant ST95.