We present a closely related companion identity, as follows:
$$- \frac{1}{2} \log 2 + \frac{1}{8} \pi
= \sum_{n\ge 1} \frac{1}{n} \frac{1}{\exp(\pi n) + 1}
- \sum_{n\ge 1} \frac{1}{n} \frac{1}{\exp(2\pi n) + 1}
\\ - 3 \sum_{n\ge 1} \frac{1}{n} \frac{1}{\exp(4\pi n) - 1}
+ 3 \sum_{n\ge 1} \frac{1}{n} \frac{1}{\exp(2\pi n) - 1}.$$
These sums may be evaluated
using harmonic summation techniques.
Introduce the sum
$$S(x) = \sum_{n\ge 1} \frac{1}{n} \frac{1}{e^{nx}+1}$$
with $x\ge 0.$
We start by trying to compute $S(\pi)-S(2\pi)$ as asked by the OP
and obtain the quoted identity when that strategy does not yield the
desired result.
The sum term is harmonic and may be evaluated by inverting its Mellin
transform.
Recall the harmonic sum identity
$$\mathfrak{M}\left(\sum_{k\ge 1} \lambda_k g(\mu_k x);s\right) =
\left(\sum_{k\ge 1} \frac{\lambda_k}{\mu_k^s} \right) g^*(s)$$
where $g^*(s)$ is the Mellin transform of $g(x).$
In the present case we have
$$\lambda_k = \frac{1}{k}, \quad \mu_k = k
\quad \text{and} \quad
g(x) = \frac{1}{e^x+1}.$$
We need the Mellin transform $g^*(s)$ of $g(x)$ which is
$$\int_0^\infty \frac{1}{e^{x}+1} x^{s-1} dx
= \int_0^\infty \frac{e^{-x}}{1+e^{-x}} x^{s-1} dx
\\ = \int_0^\infty \sum_{q\ge 1} (-1)^{q+1} e^{-q x} x^{s-1} dx
= \sum_{q\ge 1} (-1)^{q+1} \int_0^\infty e^{-q x} x^{s-1} dx
\\= \Gamma(s) \sum_{q\ge 1} \frac{(-1)^{q+1}}{q^s}
= \left(1-2\frac{1}{2^s}\right)\Gamma(s) \zeta(s).$$
It follows that the Mellin transform $Q(s)$ of the harmonic sum
$S(x)$ is given by
$$Q(s) = \left(1-\frac{1}{2^{s-1}}\right)
\Gamma(s) \zeta(s) \zeta(s+1)
\\ \text{because}\quad
\sum_{k\ge 1} \frac{\lambda_k}{\mu_k^s} =
\sum_{k\ge 1} \frac{1}{k} \frac{1}{k^s}
= \zeta(s+1)$$
for $\Re(s) > 1.$
The Mellin inversion integral here is
$$\frac{1}{2\pi i} \int_{3/2-i\infty}^{3/2+i\infty} Q(s)/x^s ds$$
which we evaluate by shifting it to the left for an expansion about
zero.
The two zeta function terms cancel the poles of the gamma function
term, the factor in front the pole of the first zeta function term and
we are left with just
$$\begin{align}
\mathrm{Res}(Q(s)/x^s; s=0) & =
- \frac{1}{2} \log 2 + \frac{1}{2} \log\pi - \frac{1}{2} \log x
\quad\text{and}\\
\mathrm{Res}(Q(s)/x^s; s=-1) & = \frac{x}{8}
\end{align}$$
This shows that
$$S(x) = - \frac{1}{2} \log 2 + \frac{1}{2} \log\pi -\frac{1}{2} \log x
+ \frac{x}{8}
+ \frac{1}{2\pi i} \int_{-3/2-i\infty}^{-3/2+i\infty} Q(s)/x^s ds.$$
To treat the integral recall the duplication formula of the gamma
function:
$$\Gamma(s) =
\frac{1}{\sqrt\pi} 2^{s-1}
\Gamma\left(\frac{s}{2}\right)
\Gamma\left(\frac{s+1}{2}\right).$$
which yields for $Q(s)$
$$\left(1-\frac{1}{2^{s-1}}\right)
\frac{1}{\sqrt\pi} 2^{s-1}
\Gamma\left(\frac{s}{2}\right)
\Gamma\left(\frac{s+1}{2}\right)
\zeta(s) \zeta(s+1)$$
Furthermore observe the following variant of the functional equation
of the Riemann zeta function:
$$\Gamma\left(\frac{s}{2}\right)\zeta(s)
= \pi^{s-1/2} \Gamma\left(\frac{1-s}{2}\right)
\zeta(1-s)$$
which gives for $Q(s)$
$$\left(1-\frac{1}{2^{s-1}}\right)
\frac{1}{\sqrt\pi} 2^{s-1}
\pi^{s-1/2}
\Gamma\left(\frac{s+1}{2}\right)
\Gamma\left(\frac{1-s}{2}\right)
\zeta(1-s)\zeta(s+1)
\\ = \left(1-\frac{1}{2^{s-1}}\right)
\frac{1}{\sqrt\pi} 2^{s-1}
\pi^{s-1/2}
\frac{\pi}{\sin(\pi(s+1)/2)}
\zeta(1-s)\zeta(s+1)
\\ = \left(1-\frac{1}{2^{s-1}}\right)
2^{s-1}
\frac{\pi^s}{\sin(\pi(s+1)/2)}
\zeta(1-s)\zeta(s+1).$$
Now put $s=-u$ in the remainder integral to get
$$\frac{1}{2\pi i} \int_{3/2-i\infty}^{3/2+i\infty}
\left(1-2^{u+1}\right)
2^{-u-1}
\\ \times \frac{\pi^{-u}}{\sin(\pi(-u+1)/2)}
\zeta(1+u)\zeta(1-u) x^u du
\\ = \frac{1}{2\pi i} \int_{3/2-i\infty}^{3/2+i\infty}
\left(1-2^{u+1}\right)
2^{-u-1}
\\ \times \frac{\pi^{u}}{\sin(\pi(-u+1)/2)}
\zeta(1+u)\zeta(1-u) (x/\pi^2)^u du.$$
Now $$\sin(\pi(-u+1)/2) = \sin(\pi(-u-1)/2+\pi)
\\ = - \sin(\pi(-u-1)/2) = \sin(\pi(u+1)/2)$$
and furthermore
$$(1-2^{u+1}) 2^{-u-1}
= \left(\frac{1}{2^{u+1}} - 1\right)
= \left(\frac{4}{2^{u+1}} - 1\right)
- \frac{3}{2^{u+1}}.$$
We have shown that
$$S(x) = - \frac{1}{2} \log 2 + \frac{1}{2} \log\pi - \frac{1}{2}\log x
+ \frac{x}{8} - 2 S(2\pi^2/x)
\\ - 3 \frac{1}{2\pi i}
\int_{3/2-i\infty}^{3/2+i\infty}
\Gamma(u) \zeta(u) \zeta(u+1)
(x/\pi^2/4)^u du$$
or alternatively
$$S(x) = - \frac{1}{2} \log 2 + \frac{1}{2} \log\pi - \frac{1}{2}\log x
+ \frac{x}{8} - 2 S(2\pi^2/x)
- 3 T(4\pi^2/x)$$
where
$$T(x) = \sum_{n\ge 1} \frac{1}{n}
\frac{1}{\exp(nx)-1}$$
with functional equation
$$T(x) = - \frac{1}{24} x - \frac{1}{2}\log 2 - \frac{1}{2}\log\pi
+ \frac{1}{2}\log x + \frac{\pi^2}{6x} + T(4\pi^2/x).$$
This implies that (evaluate at $\pi$ and $4\pi$)
$$T(\pi)-T(4\pi) = -\frac{1}{2}\log 2 + \frac{1}{8}\pi.$$
We seek $S(\pi)-S(2\pi)$ and obtain
$$S(\pi)-S(2\pi) = -\frac{1}{2} \log \pi
+ \frac{1}{2} \log \pi + \frac{1}{2} \log 2
+ \frac{\pi}{8} - \frac{\pi}{4}
\\ - 2 (S(2\pi)-S(\pi)) - 3 (T(4\pi) -T(2\pi)).$$
This says that
$$S(\pi)-S(2\pi) = -\frac{1}{2}\log 2 + \frac{\pi}{8}
+ 3(T(4\pi)-T(2\pi)).$$
which is the claim.
Addendum. Working directly with the term
$$\left(\frac{1}{2^{u+1}} - 1\right)$$
we obtain the alternate equation
$$S(x) = - \frac{1}{2} \log 2 + \frac{1}{2} \log\pi - \frac{1}{2}\log x
+ \frac{x}{8} - 2 T(2\pi^2/x)
+ T(4\pi^2/x)
\\ = \frac{1}{6} x + \log\pi - \log x - \frac{\pi^2}{6x}
+ T(x)- 2 T(2\pi^2/x)$$
which yields
$$S(\pi)-S(2\pi) = \log 2 - \frac{1}{4}\pi
+ 3(T(\pi)-T(2\pi)).$$