The potential uses and therapeutic benefits of RNA interference (RNAi) are enormous. Recent insights into RNAi technologies have highlighted their role in analyzing the functions and regulation of gene expression in eukaryotes and further utilizing this information for identification and amelioration of many diseases. These studies have also established the role of RNAi mediated post-transcriptional gene silencing (PTGS) mechanism in mammals by several endogenous, gene regulation systems including small interfering RNAs (siRNA), micro RNA (miRNA) and small hairpin RNAs (shRNA). Moreover, these RNAi-based therapeutics have demonstrated the capability to silence therapeutically relevant genes in various in vivo models of cancer, infections autoimmune diseases and other genetic disorders. Over the past few decades, infectious diseases have been one of the leading causes of death around the world. Ubiquitously, intracellular obligate or facultative microorganisms cause serious or fatal infections and associated diseases in humans. Currently available literature suggests that infections caused by intracellular pathogens present an intriguing area, wherein RNAi technology may be effectively employed to neutralize the harmful effects of various intracellular pathogens. In this manuscript, we have emphasized on the challenges and opportunities involved in the therapy of such intracellular infections, especially employing RNAi-based interventions. We have focused our discussion on the current state-of-the-art RNAi-based therapies, which have been explored for various intracellular infections mediated by bacteria, fungi, viruses and protozoa. Nanocarrier mediated delivery of siRNA and shRNA molecules have also been found to overcome the various delivery challenges of these biotherapeutics; these have also been briefly summarized here. Furthermore, the outcomes and progresses that have been made in pre-clinical models and clinical trials have also been presented to review the numerous challenges encountered so far. Finally, we have also addressed the various future perspectives that could overcome these challenges and accelerate the progress and commercial success of these systems.