We report 0.8–2.5 μm spectrophotometry of CI Aquilae at eight epochs between 2000 May 9 and 2001 June 2 UT, corresponding to approximately 3 and 391 days after peak brightness. Near peak brightness, the spectra showed emission lines that were characteristic of a low-excitation, nitrogen-rich shell. Within a few weeks, the spectra began to show higher excitation/ionization emission lines indicative of a harder illuminating source: the neutral metal lines faded, leaving only lines of H I, He I, and He II and the emerging coronal lines. A month after peak brightness, the [Ca VIII] coronal line at 2.3205 μm appeared and persisted until the last of our observations, on day +391. From the O I line ratios, we deduced a reddening of EB-V = 1.5 ± 0.1 and a visual extinction of AV = 4.6 ± 0.2. Along with the rate of decline from the light curve (t2), we derived a distance of 2.6 ± 1.3 kpc. The frequently observed unidentified novae lines were present in CI Aquilae along with a potentially new member of the group at 2.425 ± 0.002 μm.