Metrans Rail was originally established under the name Railtrans by Petr Šimral and Radan Stift, a pair of locomotive drivers, in August 2003.

[5] On 6 May 2013, Metrans opened its new container terminal at Česká Třebova, Eastern Bohemia; built at a cost of €16.5 million, the facility became the second hub of the company's intermodal operations.

[10] Possessing six 630m-long electrified sidings and three gantry cranes, it had sufficient capacity to handle around 150 trains per week travelling to and from destinations such as Austria, Slovakia, and Hungary.

[10] By September 2014, Metrans was reportedly operating up to seven intermodal trains per day in both directions between the port of Hamburg and terminals in Prague and Ceska Trebova in the Czech Republic.

[16] During September 2014, the first of an order for 20 Traxx MS locomotives was delivered to Metrans by Bombardier Transportation; the new fleet was intended for use on its intermodal services from Hamburg and Bremerhaven to the Czech Republic, Slovakia and Hungary, and were envisioned as reducing the company's operating costs.

[11] In February 2016, Metrans awarded Alstom a contract for two Prima H3 hybrid locomotives; they will be used for shunting and are expected operate between 50 and 75 percent of the time purely on battery power.

[18] During November 2019, Metrans Rail accepted delivery of the first of ten Siemens Vectron locomotives for its transnational freight services across central and eastern Europe; accordingly, they are certified to operate in Austria, the Czech Republic, Germany, Hungary, Poland, Slovakia and Slovenia with the corresponding national signalling apparatus in addition to ETCS equipment.