Cyanoacetylene molecules are widespread in the interstellar medium (ISM) and several of its isomers have been detected in cold molecular clouds and circumstellar gas. Accurate estimates of the abundance ratio of cyanoacetylene isomers may provide deep insight into their environment. Such knowledge requires rigorous modelling of the emission spectra based on non-local thermodynamic equilibrium (LTE) radiative transfer calculations. To this end, we computed excitation cross-sections of HC2NC and HNC3 induced by collision with para- and ortho-H2, using a quantum mechanical close-coupling method. Then, by thermally averaging these data, we derived rate coefficients for the first 31 low-lying rotational levels of each isomer for temperatures up to 80 K. For the para-H2 collider, the propensity rules are in favour of rotational transitions involving Δj1 = 2 for both isomers, while for the ortho-H2 collider, Δj1 = 2 and Δj1 = 1 rotational transitions are favoured for HC2NC and HNC3, respectively. A comparison of rate coefficients for the HC3N isomers shows differences up to an order of magnitude, especially at low temperatures. Finally, we performed non-LTE radiative transfer calculations to assess the impact of such variations in the analysis of observations. Our simulation suggests that the lack of collisional data specific to each isomer could lead to errors up to a factor of 2–3 in the excitation temperatures. We expect that these data could help in better understanding the cyanoacetylene chemistry and constraining the nitrogen chemistry in the ISM.