The rampage in Georgia has reverberated across this nation of 52 million, which in the decades since the Korean War has had a deep and enduring relationship with the U.S. The two are allies and share close cultural ties.

It can often seem like every Korean knows someone with relatives or friends living in the U.S. South Korea sends more of its children to study in America than in any other foreign country.

Lee Myung-kyu, a 55-year-old office worker, said he knows many South Korean families who have dreamed of immigrating to the U.S., hoping for a better life. His own daughter wants to go to school in America. But Mr. Lee said he now has doubts.

“I keep thinking about whether something like this could happen to her,” Mr. Lee said.

Local police say the white man from Georgia charged with murder in the case said he was driven by what he called a sex addiction. Authorities say they are investigating whether the killings were racially motivated.

The attack has sparked fear at the same time police and government officials in New York and other U.S. cities have said hate crimes against Asian-Americans have risen since the start of the Covid-19 pandemic, which first emerged in China.

Han Ye-rim, 32, said she has long idealized the U.S. as a diverse society. But staring at a victim list that looks much like herself, Ms. Han wonders how she would actually fare leaving Seoul.

“Learning about the Atlanta incident was a wake-up call to me,” Ms. Han said. “I’m realizing that I can be targeted for being different if I leave this country.”

What made the Atlanta rampage especially jarring was how good South Koreans, and Korean-Americans, had been feeling lately about their standing in the U.S.

U.S. Secretary of State Antony Blinken and Defense Secretary Lloyd Austin visited Korea on their first foreign trip. Barely a year ago, the South Korean film “Parasite” emerged with an unprecedented Best Picture win at the Academy Awards. BTS, the Korean pop band, had recently performed at the Grammys and topped Billboard’s album charts.

Meanwhile, South Koreans had rushed to the local box office to see the U.S. film “Minari,” which depicts a new Korean immigrant family in rural Arkansas and was itself just nominated for several Oscars.

“It’s really a weird kind of dichotomy,” said Abraham Kim, executive director for the Council of Korean Americans, a Washington-based nonprofit group, with celebrations of pop culture on the one hand and what he described as Asians “being targeted for violence on the other.”

South Korean media has given widespread coverage to the Atlanta shootings. In a Thursday editorial, Kyunghyang Shinmun, a left-leaning newspaper, called American society “defenseless to racist attacks.” Another outlet, the right-leaning Segye Ilbo, urged the U.S. to take “effective measures so that crimes against humanity do not take root.”

On Friday, President Biden, saying that the investigation is still under way, mourned the victims and declared that “hate can have no safe harbor in America.”

South Korean President Moon Jae-in has called the Atlanta killings shocking, while the country’s foreign ministry supported the U.S. government’s efforts to stand against hatred and violence. “Such a crime is unacceptable under any circumstances,” the foreign ministry said in a Saturday statement.

Walking with a friend just blocks from the U.S. Embassy in Seoul, where the American flag continues to fly at half-staff in honor of the shooting victims, Yoon Ji-a recalled living in California during her youth. Her parents had a few brushes with racism, she said. But the events in Atlanta caught her by surprise.

“It’s scary,” said Ms. Yoon, a 20-year-old college student.

There are about 1.8 million Korean-Americans, according to the U.S. figures. The biggest Korean populations are in the metropolitan areas of Los Angeles, New York and Washington, D.C., according to Pew Research Center figures, analyzing U.S. data. Atlanta ranks seventh-largest.

Jean Lee has two children living in the U.S., though she hadn’t learned of the Atlanta-area shootings until local media began broadcasting coverage of the weekend protests and vigils across nearly two dozen American cities. Now the 48-year-old fears her children could be targeted.

“A lot of hate speech surfaced when people began calling the coronavirus the ‘Wuhan virus’ and it’s unfortunate that this issue came to light because of the shootings,” Ms. Lee said. “It feels late for Asians who have been experiencing discrimination for so long.”

Jenna Lee, a 25-year-old online shopping-mall owner, said she lived in Atlanta for two years as a teenager. In recent days, she said, she watched “Minari,” with its tale of struggling immigrants, and it prompted her to wonder whether Asian-Americans would be forever foreign and forever invisible.

“Asians are more than just people trying to assimilate into American society,” Ms. Lee said. And in her view, she said, “the shootings show how vulnerable we are to discrimination.”

Write to Timothy W. Martin at timothy.martin@wsj.com and Dasl Yoon at dasl.yoon@wsj.com