"Spring is Coming" is the title of the performances by the troupe, which come ahead of an inter-Korean summit slated for April 27.
The visit, described by many as a cultural charm-offensive by the South, came as a diplomatic thaw quickens on the peninsula after months of military tensions.
A 70-member technical crew arrived in the North on Thursday in preparation for the concerts.
The all-female quintet was announced as part of a South Korean art troupe that will stage two performances in Pyongyang on Sunday and Tuesday.
Kim Jong Un, his wife, Ri Sol Ju, and his younger sister, Kim Yo Jong were among the 1,500 spectators.
A South Korean artistic group including K-pop singers flew to Pyongyang on Saturday for two performances in the North Korean capital.
South Korean artists pose for a photo at the Pyongyang International Airport on Saturday.
Kim followed up by agreeing to a summit with the South's President Moon Jae-in, and reportedly to another with US President Donald Trump.
He met Chinese President Xi Jinping in Beijing last week during his first overseas trip.
The leaders of the two countries are scheduled to meet for a summit on April 27, the first in more than a decade. Riding on the momentum, North Korea is set to hold talks with the United States on denuclearization before the end of May.
Such deployments during past drills has frequently drawn an angry response from Pyongyang. As a result, the singer will not take part in the concert.
The group shot to stardom in 2009, making Seohyun one of today's most recognisable K-pop singers.
It was unclear whether Kim Jong Un would make an appearance at the concerts. On Tuesday, the two Koreas plan to hold a joint performance.
"I told myself, 'let's do our best even if there's no response (from the audience).but they showed so much reaction", added a member called Wendy. "Unfortunately, she will not be able to attend the concert", said the source.
Joy will not be able to perform with Red Velvet in Pyongyang, North Korea.
Legendary South Korean singer Cho Yong-pil, who held a solo sell-out concert in Pyongyang in 2005, was another star of the show.
In an interview with Billboard in 2013, the 68-year-old singer was dubbed a "K-pop legend". She made a surprise appearance alongside a North Korean classical music ensemble during their performance in Seoul last month.
The audiences for the concerts will consist mostly of elite, loyal cadres unlikely to undergo a sudden ideological conversion under the influence of a few K-pop stars.
The stiffened crowd refused to respond to the athletes who asked them to clap their hands to Fire - an intense electro-dance score peppered with rapid-fire rap delivered in both Korean and English.
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Chinese President Xi Jinping promised Beijing would uphold its friendship with North Korea after his meeting with Mr Kim. Trump welcomed the meeting between Kim and Xi, while calling for continued pressure against the isolated regime.