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Franklin was a prodigious inventor. Among his many creations were the lightning rod, the glass harmonica, the Franklin stove, bifocal glasses, and the flexible urinary catheter. Franklin never patented his inventions; in his autobiography he wrote, "... as we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." His inventions also included social innovations, such as paying forward. As deputy postmaster, Franklin became interested in the North Atlantic Ocean circulation patterns which carried mail ships. Franklin worked with Timothy Folger, his cousin and experienced Nantucket whaler captain, and other experienced ship captains, learning enough to chart the Gulf Stream, giving it the name by which it's still known today. It took many years for British sea captains to follow Franklin's advice on navigating the current, but once they did, they were able to gain two weeks in sailing time. In 1743, Franklin founded the American Philosophical Society to help scientific men discuss their discoveries and theories. He began the electrical research that, along with other scientific inquiries, would occupy him for the rest of his life, in between bouts of politics and moneymaking.

In 1748, he retired from printing and went into other businesses. He created a partnership with his foreman, David Hall, which provided Franklin with half of the shop's profits for 18 years. This lucrative business arrangement provided leisure time for study, and in a few years he had made discoveries that gave him a reputation with the educated throughout Europe and especially in France. His discoveries included his investigations of electricity. Franklin proposed that "vitreous" and "resinous" electricity were not different types of "electrical fluid" (as electricity was called then), but the same electrical fluid under different pressures. He was the first to label them as positive and negative respectively, and he was the first to discover the principle of conservation of charge.

In 1750, he published a proposal for an experiment to prove that lightning is electricity by flying a kite in a storm that appeared capable of becoming a lightning storm. On May 10, 1752, Thomas-François Dalibard of France conducted Franklin's experiment (using a 40-foot-tall iron rod instead of a kite) and extracted electrical sparks from a cloud. On June 15, Franklin may have possibly conducted his famous kite experiment in Philadelphia and also successfully extracted sparks from a cloud, although there are theories that suggest he never performed the experiment. Franklin's experiment was not written up until Joseph Priestley's 1767 History and Present Status of Electricity; the evidence shows that Franklin was insulated (not in a conducting path, since he would have been in danger of electrocution in the event of a lightning strike). (Others, such as Prof. Georg Wilhelm Richmann of Saint Petersburg, Russia, were electrocuted during the months following Franklin's experiment.) In his writings, Franklin indicates that he was aware of the dangers and offered alternative ways to demonstrate that lightning was electrical, as shown by his use of the concept of electrical ground.

If Franklin did perform this experiment, he did not do it in the way that is often described, flying the kite and waiting to be struck by lightning, as it would have been fatal. Instead, he used the kite to collect some electric charge from a storm cloud, which implied that lightning was electrical. On October 19 in a letter to England explaining directions for repeating the experiment, Franklin wrote: "When rain has wet the kite twine so that it can conduct the electric fire freely, you will find it streams out plentifully from the key at the approach of your knuckle, and with this key a phial, or Leiden jar, maybe charged: and from electric fire thus obtained spirits may be kindled, and all other electric experiments [may be] performed which are usually done by the help of a rubber glass globe or tube; and therefore the sameness of the electrical matter with that of lightening completely demonstrated."

Franklin's electrical experiments led to his invention of the lightning rod. He noted that conductors with a s harp rather than a smooth point were capable of discharging silently, and at a far greater distance. He surmised that this knowledge could be of use in protecting buildings from lightning, by attaching "upright Rods of Iron, made sharp as a Needle and gilt to prevent Rusting, and from the Foot of those Rods a Wire down the outside of the Building into the Ground;...Would not these pointed Rods probably draw the Electrical Fire silently out of a Cloud before it came nigh enough to strike, and thereby secure us from that most sudden and terrible Mischief!" Following a series of experiments on Franklin's own house, lightning rods were installed on the Academy of Philadelphia (later the University of Pennsylvania) and the Pennsylvania State House (later Independence Hall) in 1752.

In recognition of his work with electricity, Franklin received the Royal Society's Copley Medal in 1753, and in 1756 he became one of the few eighteenth century Americans to be elected as a Fellow of the Society. The cgs unit of electric charge has been named after him: one franklin (Fr) is equal to one statcoulomb. On October 21, 1743, according to popular myth, a storm moving from the southwest denied Franklin the opportunity of witnessing a lunar eclipse. Franklin was said to have noted that the prevailing winds were actually from the northeast, contrary to what he had expected. In correspondence with his brother, Franklin learned that the same storm had not reached Boston until after the eclipse, despite the fact that Boston is to the northeast of Philadelphia. He deduced that storms do not always travel in the direction of the prevailing wind, a concept which would have great influence in meteorology.

Franklin noted a principle of refrigeration by observing that on a very hot day, he stayed cooler in a wet shirt in a breeze than he did in a dry one. To understand this phenomenon more clearly Franklin conducted experiments. On one warm day in Cambridge, England, in 1758, Franklin and fellow scientist John Hadley experimented by continually wetting the ball of a mercury thermometer with ether and using bellows to evaporate the ether. With each subsequent evaporation, the thermometer read a lower temperature, eventually reaching 7 °F (-14 °C). Another thermometer showed the room temperature to be constant at 65 °F (18 °C). In his letter "Cooling by Evaporation," Franklin noted that “one may see the possibility of freezing a man to death on a warm summer’s day."

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