Investigation of the intracellular fate of small interference RNA (siRNA), after their delivery into cells by nanoparticles, is of great interest to the development of more efficient methods for transfection of siRNA. The fluorescence resonance energy transfer (FRET) based method using upconversion fluorescent nanoparticles (UCN) as energy donor is established to study intracellular release and biostability of siRNA in live cells. The UCN/siRNA-BOBO3 complex is prepared where BOBO-3-stained siRNAs are attached to the surface of amino-group-modified silica/NaYF(4):Yb,Er UCN. The energy is transferred from the UCN donor to the BOBO-3 acceptor under excitation of a near-infrared (NIR) laser. The FRET efficiency is established as a reliable parameter to follow the release and biostability of siRNA in phosphate buffered saline (PBS) and live cells. Intracellular FRET analysis shows that siRNA is gradually released into cells for a duration of 24 h, which is confirmed by confocal microscopy colocalization measurements. The application of this straightforward and sensitive upconversion FRET technique can gain real-time information on intracellular fate of siRNA and provide a bright outlook for in vitro and even in vivo detection of biological molecules.