The 6.7bln euro ($7.3bln), 450km (280 mile) Haramain Railway linking the two holiest cities in Islam - Mecca and Medina - with the Red Sea coastal city of Jeddah, was opened last September, Reuters reported.
It shuttles passengers at speeds as fast as 300km per hour (186mph).
The fire department was fighting the blaze with air support and had brought many sections of the blaze under control, Deutsche Welle reported, adding that there was no immediate known cause of the fire.
The general directorate of Saudi Civil Defence said in an earlier tweet that it was working to extinguish the fire.
"Five people who sustained minor injuries because of the fire were transported to hospital," Al-Ekhbariya state television reported, according to AFP.
In a series of tweets, Jeddah's health directorate advised citizens to "stay as far away from fumes as possible". It also counselled them to "wear masks when leaving the house" to protect against the smoke and dust.
A video uploaded on Twitter by the Mecca provincial government showed plumes of grey smoke rising from what looked like the inside of the complex.
Security forces closed the main road linking Mecca and Jeddah and cordoned off the site, according to AFP.
The blaze erupted at 12:35 pm local time (0935 GMT), according to the Haramain High Speed Rail's Twitter account.
The company later said it was temporarily suspending all trips, adding, "For the sake of the safety of travellers, trips on the high-speed Haramain line will be suspended until further notice."
King Salman inaugurated the railway in September 2018. Officials described it as the biggest transport project in the region.
In 2011, the kingdom signed a deal for a Spanish consortium to build the rail track, supply 35 high-speed trains and handle a 12-year maintenance contract.
Saudi Arabia is increasing its infrastructure spending and expanding its railways - including a $22.5bln metro system under construction in the capital Riyadh - as it seeks to diversify its oil-dependent economy.