Passengers were forced to use temporary toilets for three years after the previous block was demolished to make way for a new waiting room.
But the project was hit by delays due to bad weather, contractor and design issues.
Cllr Phil Knowles, who spearheaded the campaign, was delighted the facilities had opened but said he will keep an eye on the project until it is completed.
He said: “I met with those who worked on the scheme and had the opportunity to thank them for finally getting this over the line. The facilities are light, bright and very modern and are what you would expect in the 21st century.
“There are still bits and pieces in and around the station to finish off and we will continue to monitor and push on these but finally we have the completion of the waiting room and toilets.”
In recent years the station has undergone several improvements as part of the Midland Main Line Upgrade – the largest programme of works since it was completed in 1870.
It includes an accessible footbridge, an extended car park with 200 extra spaces and straighter tracks so trains can travel through the station at higher speeds.
Network Rail East Midlands route director Gary Walsh said: “This has been eagerly awaited by passengers who use Market Harborough station and I want to thank them for their patience.
“This work brings together the package of improvements we’ve implemented in recent years to truly transform train travel in the town.”