Fluorescence optical tomography systems have been invented to directly measure several deep tissue features. While the highly scattered nature of the signal degrades spatial resolution, this scattering process also dramatically increases the optical path length and thereby amplifies the signal sensitivity to features such as capillaries and cells, suppressing the dominance of major blood vessels. The potential for high optical contrast with centimeter-level penetration into tissue motivates sampling (i) capillary leakage with a temporal sampling of indocyanine green (ICG); (ii) mitochondrial activity with protoporphyrin IX (PpIX) intensity, and (iii) oxygen metabolism sensing with delayed fluorescence of PpIX. In this work, the single-channel prototype of an optical fiber-based tomography system was developed for these purposes. The system was comprised of two sources of laser diodes, at 633 nm and 780 nm wavelengths, two avalanche photodiode detectors, a DAQ I/O card as a control and data collection unit, and fiber cables with filter blocks, all run via LabView control. The detection fiber channels included a notch filter in each arm, at 633nm and 750nm wavelengths that act as a band stop filter for these wavelengths. Fiber cables deliver and receive light from the tissue, enabling a closed-loop passive switching system. This design has a dual-purpose channel fiber system that makes it possible to just electronically switch between sequential measurement of indocyanine green (ICG) excitation (785 nm) and protoporphyrin IX (PpIX) excitation (635 nm) without any optical component movements, while transmission of the excitation signal is implicitly measured at the opposite detector. The fluorescence-to-transmission ratio data eliminates issues of fiber coupling or tissue transmission variations. The system was validated for linearity of response in relevant biological concentration ranges for each fluorophore. Also, in vivo animal studies were carried out on a mouse to see the reliability of the system at capturing the temporal ICG kinetics. This single design of dual-channel detection is a prototype for what will be a multi-fiber tomography system that can measure the intrinsic properties of tissue coupled with ultrasound imaging.