Home prices in San Diego rose by 0.3 percent between May and June, and 6.4 percent since June 2015, according to the Standard & Poor's CoreLogic Case-Shiller Indices released Tuesday.
Only six of the 20 real estate markets covered by S&P grew at a faster pace over the past year.
The indices were created by taking the price of housing in each market in January 2000, assigning them a value of 100, and tracking their subsequent rise and fall.
San Diego stood at 225.75 in June, representing well over a doubling over nearly 17 years. Only Los Angeles and San Francisco have seen the price of housing appreciate faster.
The 20-city index was 189.87 in June, up 0.8 percent for the month and 5.1 percent for the year.
"Home prices continued to rise across the country led by the West and the South," said David Blitzer, managing director and chairman of the Index Committee at S&P Dow Jones Indices.
"In the strongest region, the Pacific Northwest, prices are rising at more than 10 percent — in the slower Northeast, prices are climbing a bit faster than inflation," Blitzer said. "Nationally, home prices have risen at a consistent 4.8 percent annual pace over the last two years without showing any signs of slowing."
He said that while sales figures for existing homes displayed a "fairly tight market," the 654,000 purchases of new single-family homes in July across the U.S. was the highest rate since November 2007, when seasonally adjusted.