This is not a full solution, but a reduction to an integral that looks a bit simpler (though I am not sure whether it admits a closed-form expression).
We integrate by parts and use the series expansion of the logarithm to obtain
$$I \equiv \int \limits_0^\infty \frac{\ln(1+x^2)}{\mathrm{e}^{\pi x}-1} \, \mathrm{d} x = \frac{2}{\pi} \int \limits_0^\infty \frac{-x \ln(1-\mathrm{e}^{-\pi x})}{1+x^2} \, \mathrm{d} x = \frac{2}{\pi} \sum \limits_{n=1}^\infty \frac{1}{n} \int \limits_0^\infty \frac{x \mathrm{e}^{-n \pi x}}{1+x^2} \, \mathrm{d} x \, .$$
Now we employ the Laplace transform identity
$$ \mathcal{L} \left(t \mapsto \frac{t}{1+t^2}\right) (p) = \sin(p) \left[\frac{\pi}{2} - \operatorname{Si}(p)\right] - \cos(p) \operatorname{Ci}(p) $$
and the representation
$$ \operatorname{Ci} (p) = \gamma + \ln(p) - \operatorname{Cin}(p)$$
of the cosine integral ($\gamma$ is the Euler-Mascheroni constant and the trigonometric integrals are defined here) to write
$$ I = \frac{2}{\pi} \sum \limits_{n=1}^\infty \frac{(-1)^{n-1}}{n} \operatorname{Ci}(n \pi) = \frac{2}{\pi} \left[[\gamma + \ln(\pi)] \ln(2) - \eta'(1) - \sum \limits_{n=1}^\infty \frac{(-1)^{n-1}}{n} \operatorname{Cin}(n \pi)\right] \, .$$
$\eta$ is the Dirichlet eta function and since $\eta'(1) = \gamma \ln(2) - \ln^2 (2) /2$ , we find
$$ I = \frac{\ln(2) \ln(2 \pi^2)}{\pi} - J \, ,$$
where
$$ J \equiv \frac{2}{\pi}\sum \limits_{n=1}^\infty \frac{(-1)^{n-1}}{n} \operatorname{Cin}(n \pi) = \frac{2}{\pi} \int \limits_0^{\pi/2} \frac{1}{t} \sum \limits_{n=1}^\infty \frac{(-1)^{n-1}}{n} [1-\cos(2 n t)] \, \mathrm{d} t \, . $$
Finally, the Fourier series of $\ln(\cos)$ yields
$$ J = \frac{2}{\pi} \int \limits_0^{\pi/2} \frac{- \ln(\cos(t))}{t} \, \mathrm{d} t = \int \limits_0^1 - \ln(s) \tan \left(\frac{\pi}{2}s\right) \, \mathrm{d} s \approx 0.59921 \, .$$
I have not found a nice expression for $J$ yet, but maybe someone else knows how to calculate this integral.
Power series expansions of the integrands lead to the following representations in terms of the Dirichlet lambda function and the dilogarithm:
$$ J = \frac{1}{\pi} \sum \limits_{n=1}^\infty \frac{\lambda(2n)}{n^2} = \frac{1}{\pi} \sum \limits_{k=0}^\infty \operatorname{Li}_2 [(2k+1)^{-2}] \, . $$