We present an atlas of Ks-band images of 206 early-type galaxies, including 160 S0-S0/a galaxies, 12 ellipticals and 33 Sa galaxies (+ one later type). The majority of the atlas galaxies belong to a magnitude-limited (mB = 12.5 mag) sample of 185 Near-InfraRed S0 Survey galaxies. To ensure that misclassified S0s are not omitted, 25 ellipticals from the Third Reference Catalogue of Bright Galaxies classified as S0s in the Carnegie Atlas were included in the sample. The observations were carried out using 34 m class telescopes with subarcsecond pixel resolution (similar to 0.25 arcsec), and were obtained in good seeing conditions (full width at half-maximum similar to 1 arcsec). The images are 23 mag deeper than Two-Micron All-Sky Survey images, allowing the detection of faint outer discs in S0s. Both visual and photometric classifications are made, largely following the classification criteria of de Vaucouleurs. Special attention is paid to the classification of lenses, which are coded in a more systematic manner than in any of the previous studies. A new lens type, called a barlens, is introduced, possibly forming part of the bar itself. Also, boxy/peanut/x-shaped structures are identified in many barred galaxies, even though the galaxies are not seen edge-on, indicating that vertical thickening is not enough to explain these structures. Photometric classification includes detection of exponential outer discs or other structures not directly visible in the images, but becoming clear in unsharp masking or residual images in decompositions. In our photometric classification, nuclear bars are assigned for 15 galaxies, which are overshadowed by bulges in visual classification. The mean Hubble stage in the near-infrared is found to be similar to that in the optical. We give dimensions of structure components, and radial profiles of the position angles and ellipticities, and show deviations from perfect elliptical isophotes. Shells and ripples, generally assumed to be manifestations of recent mergers, are detected only in six galaxies. However, multiple lenses appear in as much as 25 per cent of the atlas galaxies, which is a challenge to the hierarchical evolutionary picture of galaxies. Such models need to explain how the lenses were formed and then survived in multiple merger events that galaxies may have suffered during their lifetimes.