To fully understand the interactions of a pathogen with its host it is necessary to analyze the RNA transcripts of both the host and the pathogen throughout the course of an infection. While this can be accomplished relatively easily on the host side, the analysis of pathogen transcripts is complicated by the overwhelming amount of host RNA isolated from an infected sample. Even with the read depth provided by second-generation-sequencing, it is extremely difficult to get enough pathogen reads for an effective gene level analysis. In this study we describe a novel capture-based technique and device that considerably enriches for pathogen transcripts from infected samples. This versatile method can, in principle, enrich for any pathogen in any infected sample. To test the technique's efficacy, we performed time course tissue culture infections using Rift Valley Fever Virus and Francisella tularensis. At each time point RNA-Seq was performed and the results of the treated samples were compared to untreated controls. The capture of pathogen transcripts, in all cases, led to over an order of magnitude enrichment of pathogen reads, greatly increasing the number of genes hit, the coverage of those genes, and the depth at which each transcript was sequenced.