"CSKA that we know exists no more," Stoichkov, who was named coach of his former club earlier this month, told a news conference. "We'll start afresh, without debts."
"CSKA must now find another team with which to merge in order to use their licence and remain in Bulgaria's first division."
Former European Footballer of the Year Stoichkov said CSKA will not play in next season's Europa League despite qualifying for the competition by finishing third in the domestic table.
Speculation has been rife in local media that CSKA and four-times champions Litex Lovech could merge to save costs with the two clubs having discussed the possibility in January.
However, CSKA will play in the amateur championship next season if they fail to merge with another first division club in time for the start of the Bulgarian league on July 20.
The 31-times Bulgarian champions said in a statement that the club have transferred their 6.5 million shares to Stoichkov.
"After talks with Hristo Stoichkov, we took a common decision to transfer him all the club's shares," Dimitar Borisov, one of the club's owners, said. "We, as owners have absolutely no financial claims."
"As responsible people, we decided that Hristo Stoichkov will take the decisions about the future of the club. We took these actions because of the grave financial situation of CSKA and our inability to support the club."
CSKA have been struggling financially in recent years and have just escaped a European ban by Europe's soccer governing body UEFA over debts in the last two seasons.
The Reds were barred from the Champions League in 2008-09 after failing to meet the licencing criteria.
Many Bulgarian clubs face infrastructure difficulties and are struggling to meet administrative, legal and financial conditions laid down by UEFA.
Bulgaria's top flight will be cut by two teams to 14 next season as the domestic governing football union (BFU) tries to improve standards.
CSKA reached three European semi-finals between 1967 and 1989 but have struggled for success in recent years and have not won the league title since 2008.
Ex-Barcelona forward Stoichkov, who led Bulgaria to the 1994 World Cup semi-finals in the United States, said former leading player and coach Asparuh Nikodimov will be sporting director.
The 67-year-old crowd favourite helped CSKA win six league titles as a player between 1966 and 1975 and guided them to another five titles during three previous coaching stints.
Nikodimov also led CSKA to the European Cup semi-final in 1982 after they beat then-European champions Liverpool having knocked out holders Nottingham Forest the previous season.