The Staatsspoorwegen, the Dutch colonial railway company, chose the southern route across Java for its first major line. Connecting Cilacap, Kroya, and Yogyakarta meant crossing the limestone hills west of Gombong, where the karst terrain offered no easy passage. Beginning in 1885, workers bored a 580-meter tunnel through the rock, completing it in 1886. The finished passage was named Ijo, and the date of completion was carved above the tunnel's rim. When the full Cilacap-Kroya-Yogyakarta line opened on 20 July 1887, trains could finally run the length of Java's southern coast. For more than a century afterward, every train heading between Jakarta and Yogyakarta passed through this single narrow bore in the limestone.

The old Ijo tunnel earned a second life as a filming location. Its atmospheric portal and the dramatic approach through lush Javanese hills attracted filmmakers who used it as a backdrop for two Indonesian feature films: Kereta Api Terakhir and Daun di Atas Bantal. The tunnel's photogenic qualities also made it a favorite stop for railway enthusiasts and photographers, who would time their visits to catch trains emerging from the darkness into the green valley beyond. With some of the densest train traffic of any tunnel in Indonesia, there was rarely a long wait between crossings and overtakings.

By the 2010s, the old single-track tunnel had become a bottleneck. The Directorate General of Railways decided that doubling the track between Kroya and Kutoarjo required an entirely new bore rather than an expansion of the original. Two contractors, Wijaya Karya and Jaya Konstruksi, were engaged to build a modern tunnel running north of the old one. At 581 meters long and 9 meters in diameter, the new Ijo tunnel could accommodate two rail lines side by side. Its most distinctive technical feature was the slab track system: instead of traditional ballast and wooden sleepers, the rails sit on concrete sleepers embedded directly in a poured concrete foundation. It was the first railway tunnel in Indonesia to use this technology, eliminating the maintenance headaches that loose ballast creates in a tunnel environment.

The new tunnel and its accompanying station were partially activated on 21 April 2020, with full operations beginning on 5 May 2020 when the Kroya-Kutoarjo double track went live. On that day, the old Ijo tunnel and its adjacent station were formally deactivated. But deactivation was not demolition. The original bore, with its 1886 date still visible above the entrance, was designated a cultural heritage site. Where executive-class services like the Taksaka, Argo Dwipangga, and Argo Lawu once squeezed through the colonial-era passage, they now glide through the wider modern bore on smooth concrete. Meanwhile, the old tunnel stands silent for the first time since the 19th century, its limestone walls still bearing the marks of the laborers who carved them, a monument to the ambition that first threaded steel rails through Java's stubborn hills.