A flight deck timer management system includes a database storing conditions representing a first monitoring mode defining at least a first rule, a first timing characteristic defining a first time period for compliance with the first rule, and a first advisory value relative to the first time period at which a first advisory is initiated. A control unit is configured to identify input states based on the input data, and to evaluate the input states in view of the first monitoring mode conditions. When the input states trigger the first monitoring mode, the control unit evaluates the input states in view of the first rule, initiates a first timer based on the first timing characteristic, monitors a first timing status of the first timer relative to the first advisory value, and generates display commands representing the first advisory when the first timer status reaches the first advisory value.