KOI-13 is the first known transiting system exhibiting light-curve distortions due to gravity darkening of the rapidly rotating host star. In this Letter, we analyse publicly available Kepler Q2–Q3 short-cadence observations, revealing a continuous light variation with a period of Prot= 25.43 ± 0.05 h and a half-amplitude of 21 ppm, which is linked to stellar rotation. This period is in exact 5:3 resonance with the orbit of KOI-13.01, which is the first detection of a spin–orbit resonance in a host of a substellar companion. The stellar rotation leads to stellar oblateness, which is expected to cause secular variations in the orbital elements. We indeed detect the gradual increment of the transit duration with a rate of (1.14 ± 0.30) × 10−6 d cycle−1. The confidence of this trend is 3.85σ, and the two-sided false alarm probability is 0.012 per cent. We suggest that the reason for this variation is the expected change of the impact parameter, with a rate of d b/d t=−0.016 ± 0.004 yr−1. Assuming b≈ 0.25, KOI-13.01 may become a non-transiting object in 75–100 years. The observed rate is compatible with the expected secular perturbations due to the stellar oblateness yielded by the fast rotation.