Stress granules (SGs) form during cellular stress and are implicated in neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). To yield insights into the role of SGs in pathophysiology, we performed a high-content screen to identify small molecules that alter SG properties in proliferative cells and human iPSC-derived motor neurons (iPS-MNs). One major class of active molecules contained extended planar aromatic moieties, suggesting a potential to intercalate in nucleic acids. Accordingly, we show that several hit compounds can prevent the RNA-dependent recruitment of the ALS-associated RNA-binding proteins (RBPs) TDP-43, FUS, and HNRNPA2B1 into SGs. We further demonstrate that transient SG formation contributes to persistent accumulation of TDP-43 into cytoplasmic puncta and that our hit compounds can reduce this accumulation in iPS-MNs from ALS patients. We propose that compounds with planar moieties represent a promising starting point to develop small-molecule therapeutics for treating ALS/FTD. Display omitted Display omitted •∼100 small-molecule compounds modulate SGs in HEK293xT cells, NPCs, and iPS-MNs•ALS-associated RBPs accumulate in SGs during prolonged stress•Molecules with planar moieties disrupt accumulation of ALS-associated RBPs in SGs•Compounds reduce TDP-43 accumulation in cytoplasmic puncta in ALS mutant iPS-MNs Using high-content screening, we identified a class of planar small molecules that can (1) modulate the dynamics of neurodegeneration-linked stress granules (SGs), (2) reduce SG association of ALS-linked RNA-binding proteins, and (3) prevent accumulation of TDP-43 within persistent cytoplasmic puncta.