The agency responsible for implementing and overseeing customs regulations is the Directorate General of Customs Revenue (DGRA) which is part of the Ministry of Finance. In general a customs import declaration must be filed by an import broker.
Since February 2002, "Teledespacho," an automated system through which customs declarations can be made, has been available online. If using this system, the use of an import broker is optional.

El Salvador's customs employs a system in which goods are identified as subject to a "green light" or automatic release (5 to 20 minutes), "yellow light" or review of documents for subsequent inspection, "red light" or physical inspection for valuation purposes (2 to 24 hours). This system is applied based on parameters such as tariff classification of the goods, product origin, importer, etc.

In the event of difficulty in obtaining customs clearance due to an "irregularity" on the part of the DGRA or its representatives, the options available to the importer/exporter, as specified in the Law on Customs Simplification (Articles 15, 16, 17), are to a) reconsideration by the same customs official b) appeal before the Internal Revenue Appeals Court c) "amparo" (injunction) proceedings before the Supreme Court of Justice d) appeal for judicial review before the Supreme Court of Justice.

A Central America Integrated and Peripheral Customs Project now being implemented will allow customs clearance for several Central American countries to be done at a single customs point of entry facility. The goods cleared through customs will then be shipped on to their final destination in Central America. "Peripheral" customs facilities have been established in El Salvador, Guatemala, Honduras, and Nicaragua where customs clearance is being done for importers in Central American countries other than just the one where the facility is located.