Glasgow Royal Infirmary has sent around 1500 women for fertility treatment to a private hospital in the city since the issue came to light in November 2012.
It had been feared air pollution from nearby renovation works may have caused contamination in the sensitive fertilisation process after pregnancy rates fell by around half over about three months in late 2012.
The exact reason for what caused the drop remains unclear. However, the Human Fertilisation and Embryology Authority (HFEA), which regulates fertility treatment, has now said treatments can begin again at the unit, refurbished at a cost of £3.5 million, after it passed a crucial inspection.
The first patients are expected to begin treatment from the middle of September at the infirmary.
Patient consultations are due to resume next week.
Gwenda Burns, Scottish branch coordinator of Infertility Network Scotland, said: "The opening of the new unit is fantastic news for patients.
"Being able to access all of their treatment in this brand-new unit with its modern facilities will make a huge difference."
Jackson Carlaw MSP, Scottish Conservatives health spokesman, said the decision was an important development.
He added: "The NHS cannot afford a repeat of the problems which surfaced at the unit before.
"That's why it's so crucial that the newly refurbished unit is closely monitored to ensure it's performing to the expected standards.
"It may take some time for the unit to recover its reputation following this high-profile mess, but at least with this new approach things are moving in the right direction."
Fertility clinics must by law comply with the terms of a licence which is granted to them by the HFEA.
It carries out a full inspection every four years and interim inspections every two.
In July 2012, the organisation's inspectors were critical of a number of issues at the fertility unit. These included staff shortages.
The HFEA said its licensing officials had, after considering an inspection report last month, ruled the premises suitable for fertility treatment and approved it.
A spokesman said: "The [License] Committee was satisfied, based on evidence within the inspection report, that the centre's premises are now suitable for fertility treatment and approved the renovated premises."
A spokesman for Greater Glasgow and Clyde Health Board said it anticipated a full day-care patient clinical treatment facility, and laboratory service, will now transfer back from the private Nuffield Hospital in Glasgow, where patients had been sent, by mid-September
She said: "We are pleased that HFEA has approved a licence for the Glasgow Royal Infirmary Assisted Conception Service (ACS) following a significant £3.5millon refurbishment programme.
"The laboratory and day care patient clinical treatment facility are in the final stages of commissioning - a standard process in newly built and refurbished accommodation to test and install equipment and IT systems.
She added: "We anticipate that the full day care patient clinical treatment facility and laboratory service will transfer back to the new department at the GRI from the Glasgow Nuffield Hospital in mid-September once final commissioning has been concluded."