He started the career of historian already during studies, when his article, published in 1890 in Tomáš Garrigue Masaryk's magazine Athenaeum, proved by historical findings, that so called "Manuscript of Králův Dvůr" (Rukopis královédvorský), allegedly from the 13th century, whose authenticity has long led disputes in the Czech society, is a counterfeit.

After studies, Pekař spent one year at universities in Erlangen and Berlin, then, he taught for shorter time at the secondary school in Mladá Boleslav and Prague.

In 1897, he wrote The History of the Wallenstein conspiracy (1630–1634) and the same year, he declined sharply an anti-Czech article of German historian Theodor Mommsen, proving the importance of Czech culture for Europe; his answer was published again several times and translated into many languages.

After the end of World War I and the formation of Czechoslovakia, Pekař wrote "Czechoslovak history" (published 1921), a textbook, which was used in high schools for many years.

Janu Nepomuckém) and White Mountain (Bílá Hora) from 1921, and Fallacies and dangers of the holding reform (Omyly a nebezpečí pozemkové reformy) published in 1923.

As a historian, he reproached Masaryk for putting too much emphasis on the religious reformist significance of Czech history, while he himself stressed the aspect of nationality.

In the beginning, he considered national element as fundamental and motive, later, he spoke about complex concept of Czech history, putting it inside wider European context, being aware of complicacy and relativity of historical events.

In his view, the history of a nation cannot emerge from a single foundation, as Masaryk claimed, but is formed out of the countless layers produced by cultural, economic and political changes.