Using his newly-developed electromagnetic principle, Henry in 1831 created one of the first machines to use electromagnetism for motion. This was the earliest ancestor of modern DC motor. It did not make use of rotating motion, but was merely an electromagnet perched on a pole, rocking back and forth. The rocking motion was caused by one of the two leads on both ends of the magnet rocker touching one of the two battery cells, causing a polarity change, and rocking the opposite direction until the other two leads hit the other battery. This apparatus allowed Henry to recognize the property of self inductance. British scientist Michael Faraday also recognized this property around the same time; since Faraday published his results first, he became the officially recognized discoverer of the phenomenon.

In 1848 Henry worked in conjunction with Professor Stephen Alexander to determine the relative temperatures for different parts of the solar disk. They used a thermopile to determine that sunspots were cooler than the surrounding regions. This work was shown to the astronomer Angelo Secchi who extended it, but with some question as to whether Henry was given proper credit for his earlier work.

Prof. Henry was introduced to Prof. Thaddeus Lowe, a balloonist from New Hampshire who had taken interest in the phenomenon of lighter-than-air gases, and exploits into meteorology, in particular, the high winds which we call the Jet stream today. It was Lowe's intent to make a transatlantic crossing by utilizing an enormous gas-inflated aerostat. Henry took a great interest in Lowe's endeavors, promoting him among some of the more prominent scientists and institutions of the day. In June 1860, Lowe had made a successful test flight with his gigantic balloon, first named the City of New York and later renamed The Great Western, flying from Philadelphia to Medford, New York. Lowe would not be able to attempt a transatlantic flight until late Spring of 1861, so Henry convinced him to take his balloon to a point more West and fly the balloon back to the eastern seaboard, an exercise that would keep his investors interested. Lowe took several smaller balloons to Cincinnati, Ohio, in March 1861. On 19 April, he launched on a fateful flight that landed him in Confederate South Carolina. With the Southern States seceding from the union, and the onset of civil war, Lowe abandoned further attempts at a transatlantic crossing and, with Henry's endorsement, went to Washington to offer his services as an aeronaut to the Federal government. Henry submitted a letter to Secretary of War Simon Cameron which carried Henry's endorsement:

Hon. SIMON CAMERON:

DEAR SIR: In accordance with your request made to me orally on the morning of the 6th of June, I have examined the apparatus and witnessed the balloon experiments of Mr. Lowe, and have come to the following conclusions:

1st. The balloon prepared by Mr. Lowe, inflated with ordinary street gas, will retain its charge for several days.

2d. In an inflated condition it can be towed by a few men along an ordinary road, or over fields, in ordinarily calm weather, from the places where it is galled [i.e. swelled or inflated] to another, twenty or more miles distant.

3d. It can be let up into the air by means of a rope in a calm day to a height sufficient to observe the country for twenty miles around and more, according to the degree of clearness of the atmosphere. The ascent may also be made at night and the camp lights of the enemy observed.

4th. From experiments made here for the first time it is conclusively proved that telegrams can be sent with ease and certainty between the balloon and the quarters of the commanding officer.

5th. I feel assured, although I have not witnessed the experiment, that when the surface wind is from the east, as it was for several days last week, an observer in the balloon can be made to float nearly to the enemy's camp (as it is now situated to the west of us), or even to float over it, and then return eastward by rising to a higher elevation. This assumption is based on the fact that the upper strata of wind in this latitude is always flowing eastward. Mr. Lowe informs me, and I do not doubt his statement, that he will on any day which is favorable make an excursion of the kind above mentioned.

6th. From all the facts I have observed and the information I have gathered I am sure that important information may be obtained in regard to the topography of the country and to the position and movements of an enemy by means of the balloon now, and that Mr. Lowe is well qualified to render service in this way by the balloon now in his possession.

7th. The balloon which Mr. Lowe now has in Washington can only be inflated in a city where street gas is to be obtained. If an exploration is required at a point too distant for the transportation of the inflated balloon, an additional apparatus for the generation of hydrogen gas will be required. The necessity of generating the gas renders the use of the balloon more expensive, but this, where important results are required, is of comparatively small importance.

For these preliminary experiments, as you may recollect, a sum not to exceed $200 or $250 was to be appropriated, and in accordance with this Mr. Lowe has presented me with the inclosed statement of items, which I think are reasonable, since nothing is charged for labor and time of the aeronaut.

I have the honor to remain, very respectfully, your obedient servant,

JOSEPH HENRY,

Secretary Smithsonian Institution.

On Henry's recommendation Lowe went on to form the Union Army Balloon Corps and served two years with the Army of the Potomac as a Civil War Aeronaut.

Over 150 years ago, Henry identified the room acoustics phenomena we now call direct sound, early reflections, and reverberation. He demonstrated the early sound integration period and laid the groundwork for further fundamental research on early reflections that was not followed up until the work at Göttingen University in the 1950–1960s. He brought a robust scientific approach to the subject of acoustics. Henry devised a simple experiment to demonstrate the integration of direct and early sound. A listener, standing in an open space 100 feet from a wall, claps his hands and hears an echo. He gradually approaches the wall, clapping, until no echo is perceived, at a distance of 30 feet — the "Henry Distance" — equating to an early sound integration time of 60 ms.

As a famous scientist and director of the Smithsonian Institution, Henry received visits from other scientists and inventors who sought his advice. Henry was patient, kindly, self-controlled, and gently humorous. One such visitor was Alexander Graham Bell who on 1 March 1875 carried a letter of introduction to Henry. Henry showed an interest in seeing Bell's experimental apparatus and Bell returned the following day. After the demonstration, Bell mentioned his untested theory on how to transmit human speech electrically by means of a "harp apparatus" which would have several steel reeds tuned to different frequencies to cover the voice spectrum. Henry said Bell had "the germ of a great invention". Henry advised Bell not to publish his ideas until he had perfected the invention. When Bell objected that he lacked the necessary knowledge, Henry firmly advised: "Get it!"

On 25 June 1876, Bell's experimental telephone (using a different design) was demonstrated at the Centennial Exhibition in Philadelphia where Henry was one of the judges for electrical exhibits. On 13 January 1877, Bell demonstrated his instruments to Henry at the Smithsonian Institution and Henry invited Bell to demonstrate them again that night at the Washington Philosophical Society. Henry praised "the value and astonishing character of Mr. Bell's discovery and invention."

Henry died on 13 May 1878, and was buried in Oak Hill Cemetery in the Georgetown section of northwest Washington, D.C.