After serving with Louis Lazare Hoche and André Masséna in Germany and Switzerland (1797–99), Pajol took a cavalry command under Jean Victor Marie Moreau for the campaign on the upper Rhine.

[1] In the short years of peace Pajol, now colonel, successively served as envoy to the Batavian Republic, and delegate at Napoleon's coronation (the start of the First French Empire).

On the fall of Napoleon, Pajol gave his allegiance to the Restoration government, but he rejoined the Emperor immediately upon his return to France.

On receiving the news of the battle of Waterloo, Pajol disengaged his command, and skillfully retreated to refuge in Paris.

[1] His son, Count Charles Paul Victor Pajol (1821–1891), entered the army and reached the rank of général de division when, during the Franco-Prussian War, he was involved in the catastrophe of Metz (1870).