Naturescot confirmed the move after the majority of seabirds left the island, but some restrictions and biosecurity measures will remain in place.
It means sailings can resume from Anstruther and North Berwick.
The island, a National Nature Reserve, was closed to help protect vulnerable seabird populations from the spread and impact of the current H5N1 strain of avian flu in seabird colonies.
The breeding season is now over for most species on the Isle of May, and they have now left the island to overwinter at sea or moved to the nearby coast before migrating further afield.
Visitors will be asked to remain on paths, and biosecurity measures will be in place on boats and on the island.
The virus has been found to stay on the ground and in bird faeces for a long time, so restricting access to any areas that still have nesting seabirds and taking simple steps to disinfect boots and clean clothing is crucial.
NatureScot said it was not yet possible to assess how much the current outbreak impacted on the island’s breeding populations - some species have successfully bred.
Seabird colonies on 23 other islands around Scotland remain closed to public landings.
The position will be kept under constant review on a site-by-site basis, and restrictions will be lifted as soon as possible.
Eileen Stuart, NatureScot’s deputy director of nature and climate change, said: “We hope the restrictions limited the spread of avian flu on the Isle of May, although more research is needed to confirm this in the coming months.
“We are grateful for the ongoing support from local boat operators during this challenging period.
“On those islands which are still occupied by nesting seabirds, we’d ask for patience, as the restrictions are our best chance to reduce the spread of this deadly virus.
"We recognise that this will be disappointing for those planning a visit, but hope people understand that this is about protecting our precious seabird populations for the future. We will continue to keep the situation under regular review over the coming weeks.”