[2] In 1889 Jackson led an IBEAC expedition that included his friend and fellow explorer Arthur Neumann in the party designed to open up the regions between Mombasa and Lake Victoria, which was largely unknown to Europeans at that time, and if possible to obtain news of Emin Pasha.

At Kavirondo he received a letter from King Mwanga II of Buganda in Uganda describing a state of great confusion there owing to rivalry between different Christian factions.

He was appointed a Companion of the Order of the Bath (CB) for services during the mutiny of Sudanese troops in Uganda in 1898.

That year a paper by Jackson and Captain Shelley was published describing birds collected during his 1884–1886 trip to Africa.

After retiring, he worked on a complete history of the Birds of East Africa and Uganda, which was unpublished when he died in 1929, following pneumonia.

[2] The Birds of Kenya Colony and the Uganda Protectorate was completed by William Lutley Sclater and published in 1938.