Nishikori defeated Mikhail Kukushkin of Kazakhstan 6-3, 3-6, 6-3, 6-4 to reach the last eight for the second successive year.
The 29-year-old Japanese star trails Federer 3-7 in career meetings although he won their most recent meeting at the ATP Finals in London at the end of last season.
Monday's win was Nishikori's ninth in nine meetings against world 58 Kukushkin.