As a philosopher, he is remembered as a founding figure in the emergence of the New Left in Japan, and as a critic, he was at the forefront of a movement to force writers to confront their responsibility as wartime collaborators.

[3][4] Yoshimoto was invited to give speeches at Zengakuren meetings in December 1959 and January 1960, and he joined the student activists in a sit-in at Shinagawa Station in Tokyo as part of a nationwide general strike against the Treaty on June 4, 1960.

[6] Yoshimoto concluded that the only path forward was to reject the oppression of existence and pursue absolute individual autonomy (jiritsusei).

[6] In September 1961, Yoshimoto co-founded the magazine Experiment (Shikkō) with like-minded activists Tanigawa Gan and Murakami Ichiro, as a place to publish essays and criticism completely independently of any established organization.

The journal published articles by Miura Tsutomu, who had been expelled from the Communist Party after the critique of Stalin, his disciple Takimura Ryuichi, Nango Tsugumasa, and others.

In these and other essays, Yoshimoto developed an independent theory of the arts in the face of criticisms of the Communist Party and sectarian literary theories, emphasizing the aesthetics of language and psychological phenomena, and his concept of "communal fantasy" (共同幻想, kyōdō gensō), describing how the propaganda and militarism of the wartime era "swept away virtually the entire population in a wave of war frenzy".

[7][8] Yoshimoto's philosophy of radical individualism became a refuge for students and intellectuals exasperated by the then-current sectarian and bureaucratic Marxism.

As a result, Yoshimoto's anti-sectarian philosophy of independence and individualism became a major influence and theoretical resource in the 1960s and 1970s for the Zengakuren, Zenkyoto, and other 'non-sect' New Leftists.

Yoshimoto was a wide-ranging author who wrote on literature, subculture, politics, society, and religion (including Shinran and the New Testament).

He published many dialogues with overseas intellectuals visiting Japan, such as Michel Foucault, Félix Guattari, Ivan Illich, and Jean Baudrillard.