Consumers in the granite city, perhaps buoyed by the strong oil and gas industry, helped the shop record an 11.5% sales rise in the seven days to October 5.
That put it ahead of closest challengers such as Croydon, Chester and Cardiff.
The John Lewis store in Glasgow saw sales drop 0.7% while Edinburgh was down by 0.2%.
In the 10 weeks of the company's financial year Aberdeen is running 5.3% ahead, Glasgow is 2.9% up and Edinburgh has seen 4.2% sales growth.
Sales across all outlets and online operations were up 2.8% in the week from almost £70m to £71.9m and tracking 5.8% ahead in the 10 week trading period.
Ed Connelly, buying director, said warmer weather had affected sales in the most recent week particularly of autumn and winter collections.
He added: "There was however, a positive start for our first proper week's sales of Christmas merchandise, with double-digit growth on last year, and a corresponding increase in cooking and dining. Another bright spot was lighting, up 15% on last year. Both of these results augur well for our [quarter four] sales in home departments.
"Electricals and home technology saw a good performance, with sales up 15.1% against last year and showing the sort of momentum we need as we run into the peak trading period.
"Among the winners were large electrical appliances, up nearly 18%, laptop and desktop computing, up 20% and a terrific performance from small electrical appliances, up 45%, with great strides forward in food preparation, helped perhaps by some high-profile coverage of home breadmaking habits."
Weekly sales at upmarket grocer Waitrose, the other part of the John Lewis Partnership, saw a 7.9% rise from £109.83m to more than £116m excluding petrol.
Mixed weather saw a range of buying patterns with top sellers ranging from ice-cream to custard.
Waitrose commercial director Mark Williamson said a promotion highlighting the company's pledge to be 10% cheaper for its membership card holders than rival Tesco on hundreds of branded products was paying off with growing numbers of customers taking advantage of deals.
He said pumpkin sales were up 66% year-on-year with people buying ahead of Halloween and added: "Apples, another favourite for autumn, are continuing to see huge sales growth following the launch of our seasonal British selection tray - sales for the week were 144% higher than last year.
He said barbecue meat sales rose 90%, suggesting people perhaps wanted to "enjoy a last barbecue of the year".