Protoplanetary disks drive some of the formation process (e.g., accretion, gas dissipation, formation of structures, etc.) of stars and planets. Understanding such physical processes is one of the main astrophysical questions. HD 163296 is an interesting young stellar object for which infrared and sub-millimeter observations have shown a prominent circumstellar disk with gaps plausibly created by forming planets. This study aims at characterizing the morphology of the inner disk in HD 163296 with multi-epoch near-infrared interferometric observations performed with GRAVITY at the Very Large Telescope Interferometer (VLTI). Our goal is to depict the K-band (lambda_0 ~ 2.2 um) structure of the inner rim with milliarcsecond (sub-au) angular resolution. Our data is complemented with archival PIONIER (H-band; lambda_0 ~ 1.65 um) data of the source. We performed a Gradient Descent parametric model fitting to recover the sub-au morphology of our source. Our analysis shows the existence of an asymmetry in the disk surrounding the central star of HD 163296. We confirm variability of the disk structure in the inner ~2 mas (0.2 au). While variability of the inner disk structure in this source has been suggested by previous interferometric studies, this is the first time that it is confirmed in the H- and K-bands by using a complete analysis of the closure phases and squared visibilities over several epochs. Because of the separation from the star, position changes, and persistence of this asymmetric structure on timescales of several years, we argue that it is a dusty feature (e.g., a vortex or dust clouds), probably, made by a mixing of sillicate and carbon dust and/or refractory grains, inhomogeneously distributed above the mid-plane of the disk.