Let $\omega$ be a primitive $k$th root of unity, so that for any integer $b$,
$$\frac1k\sum_{j=1}^k \omega^{bj} = \begin{cases}1,&k\mid b, \\ 0,&k\nmid b\end{cases}.$$
This allows us to write $\sum_{i=0}^{\lfloor\frac{n}{k}\rfloor}{n \choose i * k}$ as
$$ \sum_{\substack{0\le b\le n,\\b \equiv 0 \pmod k}}{n \choose b} = \sum_{b=0}^n {n \choose b} \frac1k\sum_{j=1}^k \omega^{bj} = \frac1k \sum_{j=1}^k \sum_{b=0}^n {n\choose b} \omega^{bj}.$$
The innermost sum can be recognized as just the binomial expansion for $(1+\omega^j)^n$. So that means the desired sum is simply
$$\frac1k \sum_{j=1}^k (1+\omega^j)^n.$$
Now if you're coding this you might want to put some thought into what number system to evaluate $\omega$ in. You could do it using floating-point complex arithmetic but if $n$ is large you'll get a lot of precision loss in evaluating $(1+\omega^j)^n$ (but at least the end result can be rounded to an integer, albeit one with many digits). You could alternatively evaluate over different finite fields (say $\mathbb F_p$ where $p \equiv 1 \pmod k$ so that admits $k$th roots of unity), and then Chinese remainder the moduli together.