Harrison built his first longcase clock in 1713, at the age of 20. The mechanism was made entirely of wood, which was a natural choice of material for a joiner. Three of Harrison's early wooden clocks have survived: the first (1713) is at the Worshipful Company of Clockmakers' collection in the Guildhall; the second (1715) is in the Science Museum; and the third (1717) is at Nostell Priory in Yorkshire, the face bearing the inscription "John Harrison Barrow". The Nostell example, in the billiards room of this stately home, has a Victorian outer case, which has been thoughtfully provided with small glass windows on each side of the movement so that the wooden workings may be inspected.

In the early 1720s, Harrison was commissioned to make a new turret clock at Brocklesby Park, North Lincolnshire. The clock still works and like his previous clocks has a wooden movement of oak and lignum vitae. Unlike his early clocks, it incorporates some original features to improve timekeeping, for example the grasshopper escapement. Between 1725 and 1728, John and his brother James, also a skilled joiner, made at least three precision longcase clocks, again with the movements and longcase made of oak and lignum vitae. The grid-iron pendulum was developed during this period. These precision clocks are thought by some to have been the most accurate clocks in the world at the time. They are the direct link to the Harrison's sea clocks. No. 1, now in a private collection, belonged to the Time Museum, USA, until the museum closed in 2000 and its collection was dispersed at auction in 2004. No. 2 is in the Leeds City Museum. It forms the core of a permanent display dedicated to John Harrison's achievements, "John Harrison: The Clockmaker Who Changed the World" and had its official opening on 23 January 2014, the first longitude related event marking the tercentenary of the Longitude Act. No. 3 is in the Worshipful Company of Clockmakers' collection.

Harrison was a man of many skills and he used these to systematically improve the performance of the pendulum clock. He invented the gridiron pendulum, consisting of alternating brass and iron rods assembled so that the different expansions and contractions cancel each other out. Another example of his inventive genius was the grasshopper escapement – a control device for the step-by-step release of a clock's driving power. Developed from the anchor escapement, it was almost frictionless, requiring no lubrication because the pallets were made from lignum vitae. This was an important advantage at a time when lubricants and their degradation were little understood.

In his earlier work on the sea clocks, Harrison was continually assisted both financially and in many other ways by George Graham, the watchmaker and instrument maker. Harrison was introduced to Graham by the Astronomer Royal Edmond Halley, who championed Harrison and his work. This support was important to Harrison, as he is supposed to have found it difficult to communicate his ideas in a coherent manner.