We report on the variability of a multi-component broad absorption line (BAL) system observed in the hyper-luminous quasar J1538+0855 at z = 3.6. Observations from the Sloan Digital Sky Survey (SDSS), Very Large Telescope (VLT), Large Binocular Telescope (LBT), and Subaru telescope taken at five different epochs, spanning 17 yr in the observed frame, are presented. We detect three (A, B, and C) CIV variable troughs exhibiting extreme velocities (∼40 000–54 000 km s⁻¹) similar to the ultra-fast outflows (UFOs) typically observed in the X-ray spectra. The A component of the BAL UFO (v_ufo ∼ 0.17c) shows strength variations, while B (v_ufo ∼ 0.15c) and C (v_ufo ∼ 0.13c) components show changes both in shape and strength, appearing and disappearing at different epochs. In addition, during the last observation on June 2021, the entire BAL system disappeared. The variability trends observed during the first two epochs (1.30 yr rest frame) in the CIV, SiIV, OVI, and NV absorption spectral regions are the same for B and C troughs, while the A component of the BAL varies independently. This suggests a change in the ionization state of the absorbing gas for B and C components and tangential motion for the A component, as the cause of this temporal behaviour. Accordingly, it is possible to provide an upper limit for distance of the gas responsible for the A component of R_out^A ≤ 58 pc and, in turn, a kinetic power of Ė_K,ufo ≤ 1.37 × 10⁴⁵ erg s⁻¹. We also obtain R_out^B,C ≤ 1.9 kpc for B and C components, which implies an upper limit estimation of Ė_K,ufo ≤ 1.94 × 10⁴⁶ erg s⁻¹ and Ė_K,ufo ≤ 1.33 × 10⁴⁶ erg s⁻¹, respectively. Future spectral monitoring with high-resolution instruments is mandatory to accurately constrain physical properties of the BAL UFO discovered in the UV spectrum of J1538+0855 and investigate its role as a promising mechanism for the origin of the extended (∼75 kpc) CIV nebula surrounding this hyper-luminous quasar.