For convenience we'll work in the hyperbolic upper half plane $H$. We are given a hyperbolic quadrilateral $Q$ with vertices $a,b,c,d$ and geodesic segment edges $[ a,b ]$ $[ b,c ]$ $[ c,d ]$ $[ d,a ]$. We are also given that $\angle abc=\angle bad=\frac{\pi}{2}$ and $\rho_H([a,d])=\rho_H([b,c])$ where $\rho_H([x,y])$ is the hyperbolic length of the geodesic segment from $x$ to $y$. Can we conclude that $\rho_H([a,b])<\rho_H([c,d])$?
It's clear that by a transformation by an isometry, we can put the segment $[a,b]$ on the imaginary axis and then the segments $[a,d]$ and $[b,c]$ will be segments of half circles with centre at $0$ and of equal length, so the points $c$ and $d$ lie on the same 'ray' extending from the origin. This clearly implies that $\alpha=\angle bcd=\angle cda$ and, by the Gauss-Bonnet Theorem, we may also deduce that $0<Area_H(Q)=2\pi-(\frac{pi}{2}+\frac{pi}{2}+\alpha+\alpha)$ and so conclude that $\alpha<\frac{\pi}{2}$ (although this can be fairly easily seen graphically).
I feel like the proof that $\rho_H([a,b])<\rho_H([c,d])$ should be obvious and hinges on the fact that $0<\alpha<\frac{\pi}{2}$, but playing around with hyperbolic trigonometric identities has just led to a rather large mess.
I should point out that this was the beginning of an attempt to prove something which I have now proved using a different method. I am, however, curious to see if this method would have worked.
I'll use upper-case letters for points, and lower-case letters for distances.
Edit. As @Daniel mentions in his own answer, the $|AD|=|BC|$ condition is unnecessary. I've revised my answer to be more general.
We have quadrilateral $\square ABCD$ with right angles at $A$ and $B$. Write $p :=|AB|$, $q =|CD|$, $r = |AD|$, $s=|BC|$ for the edge lengths; finally, let $t=|BD|$ be the length of a diagonal.
In right triangle $\triangle ABD$, the Law of Cosines and Law of Sines give us $$\cosh t = \cosh p \cosh r \qquad\qquad \sinh r = \sinh t \sin \angle ABD$$ In $\triangle CBD$, we have $$\begin{align} \cosh q &= \cosh s \cosh t - \sinh s \sinh t \cos \angle CBD \\ &= \cosh s (\cosh p \cosh r) - \sinh s ( \sinh t \sin \angle ABD ) \\ &= \cosh p \cosh r \cosh s - \sinh r \sinh s\\ &= ( 2 \sinh^2 \frac{p}{2}+1) \cosh r \cosh s - \sinh r \sinh s \\ &= 2 \sinh^2\frac{p}{2} \cosh r \cosh s + \cosh(r-s) \end{align}$$ so that $$\begin{align} 2\sinh^2 \frac{q}{2} + 1 &= 2 \sinh^2\frac{p}{2} \cosh r \cosh s + \cosh(r-s) \\[6pt] 2\sinh^2 \frac{q}{2} &= 2 \sinh^2\frac{p}{2} \cosh r \cosh s + \cosh(r-s) - 1 \\[6pt] 2\sinh^2 \frac{q}{2} &= 2 \sinh^2\frac{p}{2} \cosh r \cosh s + 2\sinh^2\frac{r-s}{2} \\[6pt] \sinh^2 \frac{q}{2} &= \sinh^2\frac{p}{2} \cosh r \cosh s + \sinh^2\frac{r-s}{2} \end{align}$$
Clearly, then, $\sinh\frac{q}{2} \ge \sinh\frac{p}{2}$, so that $q\ge p$, with equality if and only if $r=s=0$.