Calsenilin is a member of the neuronal calcium sensor (NCS) family of proteins that interacts with the presenilins. Calsenilin has been found to act as a Kv4α channel interactor and as a transcriptional repressor. We have recently shown that calsenilin can be cleaved by caspase-3 and that its cleavage separates the conserved calcium-binding domain from the variable N-terminal domain. Here, we demonstrate that calsenilin can be phosphorylated by casein kinase I and that its phosphorylation can be regulated by intracellular calcium. In addition, phosphorylated calsenilin is a substrate for serine/threonine protein phosphatase (PP) 1 and/or 2A. Phosphorylation within the N-terminal domain at Ser63, the major phosphorylation site of calsenilin, inhibits cleavage of the molecule by caspase-3. Given that the N-terminal domain of calsenilin is not conserved in the larger NCS family including other KChIP/CALP proteins, phosphorylation of calsenilin may regulate a functional role that is unique to this member of the superfamily.