Initially the train the Bombay Kurla (LTT)–Mangalore/Cochin Netravati (Cochin–Kurla) Express was plied between Bombay to Mangalore/Kochi as link via the inland Poona, Gulbarga, Guntakal, Renigunta, Krishnarajapuram, Palakkad route parting at Shornur Junction.

On March 1, 1998, the Bombay Kurla (LTT)–Mangalore/Cochin Netravati (Cochin–Kurla) Express started running via the Konkan, making it the first scheduled service that ran the length of the Konkan Railway.

As the route is completely electrified since 30 March 2022, a Royapuram or an Erode-based WAP-7 hauls the train throughout its entire journey.

The 16345/46 Netravati Express runs from Lokmanya Tilak Terminus, Thane, Panvel, Roha (Technical Halt) crew Change,Khed, Chiplun, Sangameshwar,[3] Ratnagiri, Kudal, Thivim, Karmali, Madgaon Junction, Canacona, Karwar, Kumta, Murdeshwar,Bhatkal,Byndoor Mookambika Road, Kundapur,Udupi, Surathkal, Mangalore Junction, Kasaragod, Kanhangad, Charvattur, Payyanur, Kannapuram, Kannur, Thalassery, Vadakara, Kozhikode, Parappanangadi, Tirur, Kuttippuram, Shoranur Junction, Thrissur,Aluva, Ernakulam Junction, Cherthala, Alappuzha, Ambalappuzha, Haripad, Kayamkulam Junction, Karunagappalli, Kollam Junction, Varkala Sivagiri, Thiruvananthapuram Central.

The train was upgraded to modern LHB rake on September 26, 2019, with an MPS of 130 kmph.