Right from the Sangam age, indirect taxes were a major source of Government revenue in the Madurai region. Madurai, the seat of Sangam literature, was one of the chief ancient trade and industrial centres in India. The Sangam Work Maduraikkanchi vividly describes the markets (angadi) in Madurai held during the day (nalangadi) as well as during the evenings (allangadi). The markets of Madurai were cosmopolitan with people of various ethnicities and languages crowding into the shops, including foreign merchants. This is further attested by the mention on Madurai by Greek and Roman authors. Notable among them include Periplus (Pandi Mandala), Ptolemy (Modura regia pandionis). Other famous places of commercial antiquity in Madurai region include Korkai, Saliyur, Kayal, Marungurpattinam (present day Alagankulam) and Kumari (present day Kanniyakumari). The accounts of the famous Venetian traveller Marco Polo provide a detailed description of trade and commerce in the Madurai region, particularly the pearls. With flourishing trade and commerce, there are references to taxation. An inscription of Maravarman Sundara Pandya II issued in his thirteenth year near Korkai bear some evidence to taxation. GST is called ‘Carakku matrum Sevai Vari’ in Tamil. Even in olden days, Vari was a general term for tax on the goods and services. For example, Pon Vari (Tax on Gold), Thol Vari (Tax on drummers). For the measurement of goods cubic-measures such as Kalam, Nali,Tuni,Cher and and weight-measures such as Kalanju and Tulam were used.

Central Excise duties was existing for many years. Prior to 1944 individual Acts, applicable to one or same type of commodities, levied excise duty on each such goods. In 1944, consolidating Act was passed called as the Central Excises and Salt Act, 1944 which was subsequently renamed as Central Excise Act, 1944. The main revenue yielding commodities in 1960s were Tobacco, Matches and Cement and thereafter every year few more items were added.

After independence, the Madras Central Excise Collectorate has been reorganised and Madurai Central Excise Collectorate was created in 1971. Shri L S Marthandam served as the Collector of Madurai Central Excise from 1st April 1971. At that time, the jurisdiction of Madurai Central Excise Collectorate was vast. With effect from 1st April 1971, the Pondicherry Customs and Central Excise Divisional office was placed under the control of Collector of Central Excise, Madurai. However, the status quo ante was restored subsequently and Pondicherry was attached to the Madras Collectorate. Trichy Customs and Central Excise Collectorate came into being with effect from June 01, 1983 with the jurisdiction formed out of erstwhile Madurai and Madras Collectorates. Madurai Central Excise Commissionerate is functioning in Central Revenue Buildings, Bibikulam, Madurai. In the Central Revenue Buildings complex, a new building for the Central Excise Commissionerate was declared open on 20th April 1984. Initially there were 67 ranges in Madurai Collectorate. In 1997, two ranges of Dindigul division (Karur-I and II Ranges) were transfered to Trichy Central Excise Commissionerate. On Ist Nov.2002, a major re-organisation/bifuracation of Central Excise Commissionerate was carried out and the jurisdiction of New Tirunelveli Commissionerate was formed out from existing Madurai Commissionerate's jurisdiction.

Madurai airport was declared customs airport by the Union Finance Ministry in December 2010. In 2011, the customs administrative control of the Madurai International Airport was vested with the Madurai Central Excise Commissionerate. Jasmine, medical equipment, readymade garments, handicrafts, fruits, vegetables and granite products are being exported in large quantities from Madurai. The international cargo terminal at Madurai airport became operational from December,2017. Consequent to Customs reorganisation in 2018, Customs administrative control of the Madurai International Airport was vested with the Trichy Customs.

Central Excise revenue under Madurai Commissionerate was so far realised from the Cement, Chemicals, Plastics & Chemical products, Textiles, Sugar, Iron & Steel, Agro-processing sector, Aerated & Mineral Water, Paper & Paper Board, Pharmaceutical Products, Electrical, automobiles and accessories etc. After the introduction of Service Tax in the Finance Act, 1994, Service Tax was also realised by the Madurai Commissionerate from different types of service providers.

From July 1, 2017, GST- a new era in the history of Indirect taxes has begun. After the roll out of Goods and services Tax Act, 2017 from 01.07.2017, the territorial jurisdiction of Madurai Commissionerate was further modified on 22.06.2017. Tirunelveli Central Excise Commissionerate was attached as a Sub-Commissionerate to Madurai GST & Central Excise Commissionerate. The jurisdiction of Madurai CGST and Central Excise Commissionerate now spreads over the areas covering nine districts in the State of Tamil Nadu, namely,the districts of Madurai, Ramanathapuram, Sivagangai, Virudhunagar, Tuticorin,Tirunelveli, Kanyakumari, Theni, Dindigul (except D. Gudalur village of Palayam firka of Vedasandur taluk). The Commissionerate is located in Central Revenue Building, Madurai. It is surrounded by Thiruvananthapuram CGST Zone on the West, Coimbatore, Salem and Trichy Commissionerate on the North; Tirunelveli Sub-Commissionerate is located on the Southern part of the Madurai Commissionerate. Madurai CGST and CX Commissionerate comprises of 10 Divisions and two are at Madurai viz Madurai I and Madurai-II. The other eight Divisions are Dindigul-I, Dindigul-II,Virudhunagar, Sivakasi, Rajapalayam, Tirunelveli, Tuticorin, Kovilpatti.