Genes encoding proteins in a common regulatory network are frequently located close to one another on the chromosome to facilitate co-regulation or couple gene expression to growth rate. Contrasting with these observations, here, we demonstrate a functional role for the arrangement of Bacillus subtilis sporulation network genes on opposite sides of the chromosome. We show that the arrangement of two sporulation network genes, one located close to the origin and the other close to the terminus, leads to a transient gene dosage imbalance during chromosome replication. This imbalance is detected by the sporulation network to produce cell-cycle coordinated pulses of the sporulation master regulator Spo0A∼P. This pulsed response allows cells to decide between sporulation and continued vegetative growth during each cell cycle spent in starvation. The simplicity of this coordination mechanism suggests that it may be widely applicable in a variety of gene regulatory and stress-response settings. Display omitted Display omitted •The sporulation network detects transient gene dosage imbalance during replication•Negative feedback leads to pulsatile activation of sporulation master regulator•Pulsed response couples sporulation and DNA replication•Gene translocations eliminating pulses lead to sporulation defects The evolutionarily conserved arrangement of two critical sporulation network genes on opposite ends of the Bacillus subtilis chromosome results in a transient imbalance in their dosage during DNA replication to allow the coordination of sporulation commitment with the cell cycle.