Rail chiefs say the number is a 7 per cent increase on August 2016.
The second weekend of the Edinburgh festivals was the busiest few days of the month, with 384,000 people passing through the station in just three days.
ScotRail Alliance increased the number of services to and from Edinburgh during the festivals, including late-night journeys. The number of carriages on trains was also increased.
Edinburgh Waverley station manager Juliet Donnachie said: “For three and a half million people to have travelled through Waverley during August shows the impact of the festivals.
“Getting people to and from Edinburgh during the festivals is a massive operation and our station teams at Waverley and across the network did a great job helping customers travel about hassle-free.
“The festivals are a chance to showcase Edinburgh and the country to the world. We are delighted to have played such an important part in making the festivals a success.”