Real estate prices in Queens Brooklyn and The Bronx are on the rise.

While all five boroughs saw average home prices increase in the third quarter of 2016, compared to the year before, three boroughs set new records, according to a report released Monday from the Real Estate Board of New York.

Average prices in Brooklyn reached $891,000 in the third quarter, $523,000 in Queens and $400,000 in The Bronx — all marking the highest prices since REBNY began tracking the data 10 years ago.

Overall, the average sales price in the city jumped 11 percent over the year to $981,000, the report found, showing the market’s ability to bounce back after a “lukewarm” second quarter.

“The slight pause felt last quarter was redirected through the hot summer season and this heightened activity sets us up for a promising remainder of 2016,” John Banks III, president of REBNY, said in a statement.

Manhattan’s priciest neighborhood was Midtown East, where the ultra luxury development 432 Park Ave. helped elevate the area’s average price by 225 percent to $6.795 million. There were 24 sales recorded in the third quarter at 432 Park Ave. that averaged $20.9 million, the report noted.

While new condos get a lot of attention, older co-ops were facing a dip in demand on the Upper East Side, where the number of co-op sales dropped 15 percent. Prices, however, remained stable at $1.5 million.

Co-op prices saw their biggest increase on Roosevelt Island, jumping 97 percent to $742,000, followed by a 63 percent jump in East Harlem, where prices hit $667,000.

In Brooklyn, average condo prices rose most in Ocean Hill/Brownsville, jumping 180 percent to $423,000, and co-op price spiked in Prospect Lefferts-Gardens 52 percent to $498,000.

In Gowanus, one-to-three family home prices surged 41 percent to $2.035 million. Also, Bedford-Stuyvesant home prices increased 19 percent to $1.284 million over the past year, yet the number of sales dipped by 29 percent to 106, the report found.

Average condo prices in Queens were up 29 percent to $568,000 in Astoria. Flushing recorded the highest number of condo sales with 86 sales, up 28 percent from the year before. The average price was $518,000, up 6 percent. Co-ops in Ridgewood saw the biggest growth at 24 percent to $195,000, on average, and Fresh Meadows homes increased 27 percent to $350,000.

In the Bronx, Parkchester/Soundview average prices for condos rose 9 percent to $151,000, and the South Bronx’s Melrose/Morrisania co-ops jumped 17 percent to $236,000. Nearby in Mott Haven/Port Morris/Hunts Point, one-to-three family home prices jumped 70 percent to $520,000.

Staten Island saw its biggest increase — 81 percent — in Arrochar, where prices average $707,000.