Recently it has been shown that Bern-Carrasco-Johansson (BCJ) numerators of colour-kinematic duality for tree-level scattering amplitudes in Yang-Mills theory (coupled with scalars) can be determined using a quasi-shuffle Hopf algebra. In this paper we consider the same theory, but with higher-derivative corrections of the forms α′F3 and α′2F4, where F is the field strength. In the heavy mass limit of the scalars, we show that the BCJ numerators of these higher-derivative theories are governed by the same Hopf algebra. In particular, the kinematic algebraic structure is unaltered and the derivative corrections only arise when mapping the abstract algebraic generators to physical BCJ numerators. The underlying kinematic Hopf algebra enables us to obtain a compact expression for the BCJ numerators of any number of gluons and two heavy scalars for amplitudes with higher-derivative operators. The pure gluon BCJ numerators can also be obtained from our results by a simple factorisation limit where the massive particles decouple.
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