Pride Hebrides is taking place on the same day as Proud Ness in Inverness, where Highland Council will be flying the rainbow flag.
But Western Isles Council says it will not do the same, claiming there is nobody to take it down at weekends.
Pride Hebrides had contacted the local authority to offer them the flag for tomorrow's event but this was turned down.
A council spokesman said one of the reasons is because they receive several requests to fly flags and that, to ensure fairness and equity they have a policy on the flying of flags - but this policy does not include the flying of the pride flag.
The spokesman emphasised that the council simply does not fly flags at weekends when the council building is empty, and that the decision to refuse was nothing to do with the march.
A spokeswoman for Pride Hebrides declined to comment on the matter but said they are pleased this event to celebrate diversity in the islands has been attracting lots of positive attention.
According to the Pride Hebrides Facebook page, 156 people are intending to go to the Stornoway event and 356 have expressed an interest.
However The Reverend Graeme Craig, minister of Stornoway Free Church of Scotland, has previously condemned the event as "sad and shameful" and says it will point young people on a "wrong direction when it comes to identity, relationships and sexual fulfilment."
He has also said that the sooner society returns to "recognising basic biology and promoting faithful, monogamous, heterosexual marriage, the more content it will be."
Meanwhile, the gay pride march in Inverness is expected to draw around 2,000 people and local authority staff have been invited to join the parade.
It comes after Donald Morrison, a home mission worker with the Free Church of Scotland (Continuing) launched a petition opposing the Highland event on “biblical, religious and moral grounds.”
Several counter petitions were launched in response with thousands of people pledging their support for the march. Bill Lobban, convenor of the Highland Council, said Proud Ness was an opportunity to present Highland as an “inclusive and welcoming place to live.”
The rainbow flag will be flown at the Town House in Inverness and at the council headquarters.
Rev Peter Nimmo, minister of Old High St Stephen’s Church of Scotland in Inverness, is due to speak at the event to highlight the importance of challenging “hatred, discrimination and exclusion”.