The Smithsonian Institution was founded at Washington in 1846, and Henry was fittingly chosen its Secretary, that is, its chief executive officer.

And from that time until his death in 1878, over thirty years, he devoted himself to science in general.
He studied terrestrial magnetism and building materials.

He reduced meteorology to a science, collecting reports by telegraph, made the first weather map, and issued forecasts of the weather based upon definite knowledge rather than upon signs.

He became a member of the Lighthouse Board in 1852 and was the head after 1871.

The excellence of marine illuminants and fog signals today is largely due to his efforts.
Though he was later drawn into a controversy with Morse over the credit for the invention of the telegraph, he used his influence to procure the renewal of Morse's patent.