This marks a 3% decrease since August, when the average deposit was £9,229.
Help to Buy 2 applicants paid £150,488 in September on average compared to £226,641 in the wider market.
The average LTV for mortgage guarantee applicants was 94%, compared to 70% in the rest of the purchase market.
Brian Murphy, head of lending at Mortgage Advice Bureau, said: “The Help to Buy mortgage guarantee scheme continues to fill a void in the market in terms of affordability, offering a realistic way into the property market for buyers who are unable to save a large deposit.
“The generosity of the 95% loan to value associated with the scheme is clearly not being abused: lower earners are using the scheme to purchase lower-priced properties and are taking on much smaller levels of debt as a result.”
Help to Buy mortgage guarantee applicants had an average primary income of £31,270. If they saved 25% of this pay each month they could raise September’s average HTB2 deposit within 1.4 years.