A hexanucleotide (G4C2) repeat expansion (HRE) within intron one of C9ORF72 is the leading genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). C9ORF72 haploinsufficiency, formation of RNA foci, and production of dipeptide repeat (DPR) proteins have all been proposed as mechanisms of disease. Herein, we report the first example of disease-modifying siRNAs for C9ORF72 driven ALS/FTD. Using a combination of reporter assay and primary cortical neurons derived from a C9-ALS/FTD mouse model, we screened a panel of more than 150 fully chemically stabilized siRNA targeting different C9ORF72 transcriptional variants. We demonstrate the lack of correlation between siRNA efficacy in reporter assay versus native environment; Repeat-containing C9ORF72 mRNA variants are found to preferentially localize to the nucleus and thus C9ORF72 mRNA accessibility and intracellular localization have a dominant impact on functional RNAi. Using a C9-ALS/FTD mouse model, we demonstrate that di-valent siRNA targeting C9ORF72 mRNA variants specifically or non-selectively reduce expression of C9ORF72 mRNA and significantly reduce DPR proteins. Interestingly, siRNA silencing all C9ORF72 mRNA transcripts were more effective in removing intranuclear mRNA aggregates than targeting only HRE containing C9ORF72 mRNA transcripts. Combined, this data supports RNAi-based degradation of C9ORF72 as a potential therapeutic paradigm.