In April 1848 Rieger headed the national deputation that presented Czech demands to the Austrian government, and he was a leading Czech delegate to the Kremsier (Kroměříž) Parliament of 1848–49 that produced a short-lived constitutional draft for the Habsburg Empire. With the onset of reaction, he retired to France in voluntary exile but returned home in 1861. Thereafter, he brought out the first encyclopaedia in Czech (Slovník naučný ) and in 1861 founded the important newspaper Národní listy (“National Daily”). From 1861 he was also the leader of the Czech party in the Bohemian diet and in the lower house of the new Austrian Reichsrat (parliament); in June 1863 he initiated the boycott of the house by Czech delegates, which remained in effect almost without interruption until 1879. A series of political blunders that included his espousal of a Russian-led branch of Pan-Slavism at the Pan-Slavist congress in Moscow in 1867 and his flirtations with France during 1869–70 offended important elements within the Habsburg Empire, however, and eventually alienated the younger members of his own party.

After the Czech deputies' return to the Reichsrat in 1879, Rieger found his conservative national program, based on historic rights (Staatsrecht), calling for Bohemian autonomy within the empire and loyalty to the Habsburg crown, continually challenged by his young Czech critics; finally, in 1891, under a torrent of abuse, he lost his parliamentary seat and retired from politics. Despite the opposition he evoked, he was the most influential and effective advocate of the Czech national cause among his contemporaries. He also took great interest in the municipal government of Prague and helped promote the establishment of a national theatre and a Czech university in the city.