Objective: Fluorescence molecular tomography (FMT) can provide valuable molecular information by mapping the bio-distribution of fluorescent reporter molecules in the intact organism. Various prototype FMT systems have been introduced during the past decade. However, none of them has evolved as a standard tool for routine biomedical research. The goal of this work is to develop a software package that can automate the complete FMT reconstruction procedure. Methods: We present Smart Toolkit for Fluorescence Tomography (STIFT), a comprehensive platform comprising three major protocols: i) virtual FMT, i.e., forward modelling and reconstruction of simulated data, ii) control of actual FMT data acquisition, and iii) reconstruction of experimental FMT data. Results: Both simulation and phantom experiments have shown robust reconstruction results for homogeneous and heterogeneous tissue-mimicking phantoms containing fluorescent inclusions. Conclusion: STIFT can be used for optimization of FMT experiments, in particular for optimizing illumination patterns. Significance: This work facilitates FMT experiments by bridging the gaps between simulation, actual experiments, and data reconstruction.