Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease affecting motor neurons. A G4C2 repeat expansion in intron 1 of the C9ORF72 gene is the most common genetic cause of ALS and induces neurodegeneration by; (1) C9ORF72 loss-of-function; (2) RNA toxic gain-of-function; and (3) Gain-of-function through accumulation of toxic dipeptide repeat peptides (1). Removal of the G4C2 expansion in C9ORF72 partially ameliorates the gain-of-function mechanisms (2). Despite the recent failures of RNase H-dependent oligonucleotide drugs in C9ORF72-linked ALS clinical trials, therapeutic strategies to suppress expression of the toxic C9ORF72 variants containing the G4C2 expansion repeat still have enormous disease-modifying potential for ALS. In this project, we employed a steric-blocking antisense oligonucleotide strategy to mediate the reduction of expansion-containing C9ORF72 transcripts in C9ORF72 ALS patient dermal fibroblasts and iPSC-derived motor neurons. Splice-switching phosphorodiamidate morpholino oligomers (PMOs) targeting C9ORF72 exon 1 and intron 1 were electroporated into patient iPSC-derived motor neurons. Analysis of C9ORF72 transcript variant 3 (expansion containing), variant 2 (alternative transcript lacking the expansion), and all transcript variants were assayed by digital droplet PCR. RNA foci containing the C9ORF72 G4C2 expansion were measured in situ using complementary probes and a BasescopeTM assay. Gene expression analysis revealed that our PMOs could selectively reduce levels of variant 3 by >90% compared with the sham control and did not reduce levels of variant 2 or all transcript variants. Additionally, reduction of variant 3 also reduced formation of G4C2 expansion containing RNA foci. Here, we show evidence for PMO-induced suppression of the toxic C9ORF72 variant 3 in vitro using C9ORF72-linked ALS patient iPSC-derived motor neurons, suggesting that utilising an isoform switching mechanism of action and PMO chemistry may have therapeutic potential for C9ORF72-linked ALS, offering another opportunity for these patients.