We report here the draft genome sequences of 16 fluoroquinolone-resistant extraintestinal Escherichia coli isolates from human patients. These isolates had high MICs (32 to 256 μg/mL) for ciprofloxacin and contained point mutations in the quinolone resistance-determining region (QRDR) of both gyrA and parC that confer resistance to fluoroquinolone. The whole-genome sequence data provide a better understanding of the fluoroquinolone resistance mechanisms in these isolates and would be beneficial in source tracking these pathogens during pandemic outbreaks.