We introduce twisted relative Cuntz-Krieger algebras associated to finitely aligned higher-rank graphs and give a comprehensive treatment of their fundamental structural properties. We establish versions of the usual uniqueness theorems and the classification of gauge-invariant ideals. We show that all twisted relative Cuntz- Krieger algebras associated to finitely aligned higher-rank graphs are nuclear and satisfy the UCT, and that for twists that lift to real-valued cocycles, the K-theory of a twisted relative Cuntz-Krieger algebra is independent of the twist. In the final section, we identify a sufficient condition for simplicity of twisted Cuntz-Krieger algebras associated to higher-rank graphs which are not aperiodic. Our results indicate that this question is significantly more complicated than in the untwisted setting.