Signals of QCD instanton-induced processes are searched for in neutral current deep-inelastic scattering at the electron-proton collider HERA in the kinematic region defined by the Bjorken-scaling variable $x > 10^{-3}$, the inelasticity $0.2< y < 0.7$ and the photon virtuality $150 < Q^2 < 15000$ GeV$^2$. The search is performed using H1 data corresponding to an integrated luminosity of ~$351$ pb$^{-1}$. No evidence for the production of QCD instanton-induced events is observed. Upper limits on the cross section for instanton-induced processes between $1.5$~pb and $6$~pb, at $95%$~ confidence level, are obtained depending on the kinematic domain in which instantons could be produced. Compared to earlier publications, the limits are improved by an order of magnitude and for the first time are challenging theory predictions.