Rooms yield - room occupancy multiplied by the average achieved room rate - rose by 35.1 per cent to £73.19 in Glasgow and by 27.2 per cent to £98.47 in Edinburgh.
Inverness experienced an 11.2 per cent rise to £56.91, although Aberdeen saw a fall of 5.9 per cent to £80.95, according to the latest report by accountants and business advisers BDO LLP.
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Occupancy rates rose across Scotland with Edinburgh in the lead at 93 per cent, Glasgow on 90.9 per cent, Inverness on 90 per cent and Aberdeen on 85 per cent.
The firm said that Edinburgh’s revenue boost was driven by the end of the festivals and several conferences including Eurotox 2014; ESLCCC 2014; and the World Congress on Cancers of the Skin.
Glasgow continued its strong summer after the Commonwealth Games with more than 8,000 delegates attending the ECPR 2014 Conference and the CIRSE congress.
Alastair Rae, a partner in the property, leisure and hospitality sector at BDO, said: “These figures show the hotel sector’s positive summer has continued into the autumn.
“Edinburgh and Aberdeen had the top two revenue figures outside London during September.
“In fact, revenue in Edinburgh rose 27.2 per cent from an already high base figure, reaching £98.47, which is higher than all but the top end of the London market.
“Despite Aberdeen experiencing a fall in revenue, it still had a rooms yield of £80.95, which made it the second highest performer in the UK outside London.
“However, the decline in revenue in Aberdeen may be an early indication of a reduction in demand as the oil price continues to fall.
“The success of the sector in the city is closely aligned with the oil industry, which may be about to undergo a period of restructuring and consequently impact on the hotel sector.”
Overall, Scotland saw a 21.4 per cent increase in rooms yield to £81.49, slightly behind Wales, which had a 21.5 per cent increase to £49.91.
Rooms yield in regional UK increased by 14.7 per cent to £55.65 while in England it rose 13.1 per cent to £51.69.
Scotland had the highest occupancy level at 89.1 per cent, with regional UK at 83.6 per cent; Wales on 83.1 per cent and England at 82.8 per cent.
Mr Rae said: “The hospitality sector is an interesting barometer of the strength of the wider economy as it tends to be the first area to be cut back both in the leisure and business markets, and among the last to be reinstated when the market recovers.
“These figures reveal a hotel sector in robust good health and well on the way to having their best year since before the recession.”
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