Prioritizing checks for electronic check processing based on check characteristics, such as check values, receiving institutions associated with the checks, and/or delivery methods associated with the checks. A prioritization module of a check processing system receives information regarding multiple checks in a check processing queue. The prioritization module assigns at least one priority indicator to one or more of the checks. Each priority indicator includes information regarding a characteristic of the check to which the indicator is assigned. For example, the characteristic can be the value of the check, the receiving institution associated with the check, and/or the delivery method associated with the check. Upon determining that at least one of the checks cannot be timely processed if the checks are processed on a first in, first out basis, the prioritization module re-orders the checks for processing based on the assigned priority indicators.