In this article we prove path-by-path uniqueness in the sense of Davie [26] and Shaposhnikov [45] for SDE's driven by a fractional Brownian motion with a Hurst parameter H ∈ (0, 1 2 ), uniformly in the initial conditions, where the drift vector field is allowed to be merely bounded and measurable.Using this result, we construct weak unique regular solutions in W k,p loc [0, 1] × R d , p > d of the classical transport and continuity equations with singular velocity fields perturbed along fractional Brownian paths.The latter results provide a systematic way of producing examples of singular velocity fields, which cannot be treated by the regularity theory of DiPerna-Lyons [29], Ambrosio [2] or Crippa-De Lellis [24].Our approach is based on a priori estimates at the level of flows generated by a sequence of mollified vector fields, converging to the original vector field, and which are uniform with respect to the mollification parameter. In addition, we use a compactness criterion based on Malliavin calculus from [25] as well as supremum concentration inequalities.