Trans‐active response DNA‐binding protein of 43 kDa (TDP‐43) promotes tau mRNA instability and tau exon 10 inclusion. Aggregation of phosphorylated TDP‐43 is associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration. Casein kinase 1ε (CK1ε) phosphorylates TDP‐43 at multiple sites, enhances its cytoplasmic aggregation, and modulates its function in tau mRNA processing. To determine roles of TDP‐43 site‐specific phosphorylation in its localization, aggregation, and function in tau mRNA processing, TDP‐43 was mutated to alanine or aspartic acid at Ser379, Ser403/404, or Ser409/410 to block or mimic phosphorylation. Site‐specific phosphorylation of TDP‐43 and its mutants by CK1ε was studied in vitro and in cultured cells. Cytoplasmic and nuclear TDP‐43 and phospho‐TDP‐43 were analyzed by western blots. Aggregation of TDP‐43 was assessed by immunostaining and level of radioimmunoprecipitation assay buffer‐insoluble TDP‐43. Green florescent protein tailed with tau 3′‐untranslated region and mini‐tau gene pCI/SI9‐LI10 were used to study tau mRNA stability and alternative splicing of tau exon 10. We found that phospho‐blocking mutations of TDP‐43 at Ser379, Ser403/404, or Ser409/410 were not effectively phosphorylated by CK1ε. Compared with TDP‐43, higher level of phosphorylated TDP‐43 in the cytoplasm was observed. Phospho‐mimicking mutations at these sites enhanced cytoplasmic aggregation of TDP‐43. Green florescent protein expression was not inhibited by phospho‐blocking mutants of TDP‐43, but tau exon 10 inclusion was further enhanced by phospho‐blocking mutations at Ser379 and Ser403/404. Phosphorylation of TDP‐43 at Ser379, Ser403/404, or Ser409/410 primes its phosphorylation by CK1ε, promotes TDP‐43 cytoplasmic aggregation, and modulates its function in tau mRNA processing in site‐specific manner.