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In this work we investigate the quantitative effects of the misalignment kinetic axion on $R^2$ inflation. Due to the fact that the kinetic axion possesses a large kinetic energy which dominates its potential energy, during inflation its energy density redshifts as stiff matter fluid and evolves in a constant-roll way, making the second slow-roll index to be non-trivial. At the equations of motion level, the $R^2$ term dominates the evolution, thus the next possible effect of the axion could be found at the cosmological perturbations level, via the second slow-roll index which is non-trivial. As we show, the latter elegantly cancels from the observational indices, however, the kinetic axion extends the duration of the inflationary era to an extent that it may cause a 15$\%$ decrease in the tensor-to-scalar ratio of the vacuum $R^2$ model. This occurs because as the $R^2$ model approaches its unstable quasi-de Sitter attractor in the phase space of $F(R)$ gravity due to the $\langle R^2 \rangle $ fluctuations, the kinetic axion dominates over the $R^2$ inflation and in effect the background equation of state is described by a stiff era, or equivalently a kination era, different from the ordinary radiation domination era. This in turn affects the duration of the inflationary era, increasing the $e$-foldings number up to $5$ $e$-foldings in some cases, depending on the reheating temperature, which in turn has a significant quantitative effect on the observational indices of inflation and especially on the tensor-to-scalar ratio.