The St. Petersburg Mathematical Society was organized in 1890 and was the third mathematical society in Russia after the Moscow (1867) and the Khar'kov (1879) ones. Its first president was V. G. Imshenetskii (1890–1892), who brought forward the idea of the establishment of the Society, and after his death Yu.-K. Sokhotsky became president and kept this position until the first period of the existence of the Society was interrupted before the Revolution (apparently, in 1905).

Recreated in 1921 owing to the efforts of A. V. Vassiliev, under the name of the Petrograd Physical and Mathematical Society, the society began to play a very important role in mathematical life of the city and the country. During the second period of its work (till the next break) there were about 150 sessions. A. V. Vasiliev was president of the Society in 1921–1923, and N. M. Günter was president since 1923. An active part in the work of the society was taken by Ya. V. Uspenskii, V. I. Smirnov, B. N. Delone, G. M. Fikhtengol'ts, V. A. Steklov, A. A. Friedmann (secretary of the Society in 1923–1925), V. A. Fock, A. S. Bezikovich, S. N. Bernstein, Ya. D. Tamarkin, R. O. Kuzmin, N. I. Muskhelishvili, L. G. Loytsyanskii, B. G. Galerkin. The "Journal of the Leningrad Physical and Mathematical Society", founded by V. A. Steklov, was published since 1926 (after Steklov's death in 1926, the editorial board was headed by Ya. V. Uspenskii). At that time it was one of the few mathematical journals in the country. The victimization since late 20th of independently thinking people, in particular scientists, led to the decision of self dissolution of the society (that probably had eased fates of many mathematicians).

In 1953, the Leningrad Mathematical Seminar was organized on V. I. Smirnov's initiative. Actually, it played the role of society for several years. During that period the activity of the seminar and of the society was connected with the names of V.I.Smirnov, G.M.Fikhtengol'ts, A. A. Markov jr., A. D. Aleksandrov, I. P. Natanson, S. M. Lozinskii, L. V. Kantorovich, D. K. Faddeev, O. A. Ladyzhenskaya, Yu. V. Linnik, B. A. Venkov. It was only in 1959 that, due to the efforts of V. I. Smirnov and A. D. Aleksandrov, it became possible to organize the Leningrad Mathematical Society (now the St. Petersburg Mathematical Society). V. I. Smirnov was elected honorary president of the society, and Yu. V. Linnik president.

In 1965–1985, S. M. Lozinskii, in 1985–1989 D. K. Faddeev, and in 1990–1998 O. A. Ladyzhenskaya were presidents of the society. In 1998, A. M. Vershik became its president. At present, the society unites practically all active mathematicians of St. Petersburg as well as a number of mathematicians working abroad (see Section Members). SPbMS is a collective member of the European Mathematical Society and has tight contacts with the Moscow Mathematical Society and the American Mathematical Society.

Honorary Members of the Society: V. I. Smirnov, A. D. Aleksandrov, S. N. Bernstein, L. V. Kantorovich, A. A. Markov, M. G. Krein, S. G. Mikhlin, O. A. Ladyzhenskaya, V. A. Zalgaller, and N. A. Shanin have been elected Honorary Members of the Society.

"Proceedings of the St. Petersburg Mathematical Society" are being published since 1990.

Meetings of the society are held regularly (see reports published in on the Society website and Math-Net.Ru).

Since 1962, the "Young Mathematician prize" of the society is being awarded annually.