The Yomiuri Shimbun has three headquarters located in Tokyo, Osaka and Fukuoka. The work performed by the Tokyo, Osaka and Seibu headquarters extends beyond reporting the news to include a wide range of operations. They each have an editorial division that handles news reporting, one that proposes business solutions and produces advertising, one that handles newspaper sales, a division that is in charge of building and operating systems spanning from receiving articles to the printing and shipment of newspapers, one that handles exhibitions, sports events and other projects, and one responsible for human resources, general administration and accounting (some official bureau names differ between headquarters). The Tokyo headquarters also has the Digital Media Bureau, which handles digital services.

Under the Yomiuri Shimbun Holdings, there are three newspaper companies, the Yomiuri Giants, a leading professional baseball team, Chuokoron-Shinsha, a leader in public discourse in Japan and of the nation's publishing culture, and leisure company, Yomiuri Land. The Yomiuri Giants was established in 1934 under the auspices of then Yomiuri Shimbun President Matsutaro Shoriki, and was originally called the Dai-nippon Tokyo Yakyu Kurabu (Great Japan Tokyo Baseball Club). Chuokoron-Shinsha is a relatively new company, established in 1999 with a 100% capital investment from The Yomiuri Shimbun, which took over the business of the failing publishing company, Chuokoron-sha. Yomiuriland opened in 1949 as the Kawasaki Keiba Kurabu (horseracing club ) and joined the ranks of the group's seven core companies in 2021 after a successful tender offer (TOB) by the Yomiuri Shimbun Holdings.

The Yomiuri Shimbun Group considers these six companies together with the Yomiuri Shimbun Holdings, as its seven core companies.

In addition to the Yomiuri Giants, Chuokoron-Shinsha and Yomiuri Land, the Yomiuri Shimbun Group has a wide range of companies and organizations that operate a wide variety of businesses and social contribution services. They include The Hochi Shimbun, Yomiuri Travel Service, Yomiuri Fudousan, Yomiuri Print Media, the Yomiuri Nippon Symphony Orchestra, the Yomiuri Institute of Technology and the Yomiuri Light and Humanity Association. The Yomiuri Shimbun Holdings is also the top shareholder of Nippon Television Holdings, the parent company of Nippon Television Network Corporation and BS Nippon Corporation making Nippon Television Holdings a member of the Yomiuri Shimbun Group. Established in 1952, Nippon Television Network was Japan's first commercial broadcasting station, and it remains a dominant commercial broadcaster with a national network of 30 stations.