The station reopened at 4.45am but two of its platforms remain closed and facilities are reduced, with no lifts, toilets or step-free access, National Rail Enquiries said.
Stopping trains between London and Nottingham are back to normal, East Midlands Trains has said, but faster services will start and terminate at East Midlands Parkway.
Other affected routes include Nottingham to Worksop, with all services cancelled and a replacement bus service in place.
It is a busy day for the station, with football fans travelling to the city for Nottingham Forest's home fixture against Aston Villa, and Notts County supporters heading northeast for an away match against Lincoln City.
Jake Kelly, managing director of East Midlands Trains, said some "normal facilities" would not be available following "significant damage to the station".
"While we will be able to run many of our normal timetabled services, there will continue to be some disruption in the next few days as a result of the fire," he said.
Alternative plans are in place for several of the rail operator's services.
The fire began in a toilet at about 6.30am on Friday, quickly spreading to the roof of the station.
Around 60 firefighters were called to the scene at the height of the blaze. Incident commander Bryn Coleman said crews used breathing apparatus as they battled "some real severe conditions".
No one appears to have been injured.
Police confirmed later on Friday that they were treating the fire as a suspected arson attack.
"Inquiries have been ongoing and we now have reason to believe the fire may have been started deliberately," said Superintendent Sandra England, from British Transport Police.
"Officers are working to identify anyone who may have been involved in the incident, and we are appealing for information from members of the public."
The Grade II listed station, which has been refurbished in recent years, was built in the mid-19th century.
Details of East Midlands Trains services
:: London to Nottingham - stopping services will run as normal, while fast services will start and terminate at East Midlands Parkway
:: Liverpool to Norwich - services running as normal
:: Nottingham to Worksop - all services cancelled and a rail replacement bus service will operate
:: Matlock to Newark - services to run between Matlock and Derby only.
:: Leicester to Lincoln - services to run between Leicester and Loughborough and between Nottingham and Lincoln only
:: Nottingham to Skegness - services to run as normal
:: East Midlands Trains routes which do not run via Nottingham (Crewe, Grimsby, Lincoln to Peterborough, and Lincoln to Doncaster routes, as well as other mainline services) will operate as normal.
Source : https://news.sky.com/story/travel-disruption-continues-after-huge-fire-at-nottingham-station-11205538949