He was also the brother of Samuel Phillips Lee, a rear admiral in the United States Navy, and the brother-in-law of Montgomery Blair, the postmaster general under Abraham Lincoln.

[3] The office of Judge Advocate General had been formally discontinued on March 2, 1821, when the military establishment of the United States had been reduced.

The office was brought back on March 2, 1849, for the president to appoint a suitable captain of the army.

[2] His son, also named John Fitzgerald Lee (1848–1926), served as president of the St. Louis Bar Association, president of the David Rankin School of Mechanical Trades, and board member of the St. Louis Public Library.

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