In 1822, crews from Jesus and Brasenose raced each other to become Head of the River. One Brasenose rower apparently "caught a crab", slowing the boat. The Brasenose boat was bumped by the Jesus boat, but rowed on regardless and claimed to remain head of the river. Jesus and Brasenose men competed over which flag should be hoisted as head. One of the Brasenose crew ended the dispute by saying "Quot homines tot sententiae, different men have different opinions, some like leeks and some like onions", referring to the emblem on the Jesus oars, and it was agreed to row the race again. The Brasenose crew won the rematch. The incident has been said to be shown in an 1822 picture, which is the earliest depiction of an eights race at Oxford, painted by I. T. Serres (Marine Painter to George IV. However, the print was published on 1 March 1822 and it would have taken several months to prepare and engrave. It also shows a summer scene. Both of these points suggest that the print depicts either an imaginary scene or an unrecorded event from 1821.
Races gradually became more formalised, with regulations being introduced prohibiting colleges from using professional rowers or members of other colleges. A race for the colleges' second boats (Torpids) was introduced in 1826, and eventually boats with less than eight oars were excluded from the races. During the late 1820s and early 1830s, Jesus did not take part in races, but the college was mentioned as having a second boat by 1836. The formal foundation of the club dates from 1835. Official records of inter-college races begin in 1837. The Jesus College 1st VIII started the competition that year in second position, behind the Christ Church 1st VIII, but after being bumped on successive nights by Exeter, Balliol and Queen's colleges, Jesus took no further part in that year's competition. In 1838, the Jesus College boat rowed in last place on one evening, but then did not participate in the races again until 1844. The club's fortunes varied in the years thereafter, with the eight going up three places in one night in 1859, but not competing in 1860 and finishing in last place in 1864. From 1864 onwards, said Ernest Hardy (in his 1899 history of the college), "the boating record of the College has not been good" – the college did not take part in the races in many years, and it seldom improved its position by more than one or two places when it did participate. The college resumed regular participation in the races in 1882; although it was in last place in 1889, the college improved its position, and went up by nine places between 1894 and 1896. Hardy also commented that the 1896 Jesus College boat had a reputation of being one of the faster boats in the university. The crew entered for the Ladies' Challenge Plate at the Henley Regatta, but lost to Eton, the eventual winners.
By 1930, the college 1st VIII had reached its highest position on the river for thirty years. In 1947, the college chaplain Leslie Cross presented a new set of oars to the club. He retired that year, and the college magazine, noting that Cross had been a particularly generous supporter of the club, stated that the oars had already been used to good purpose. The 1st VIII progressed further in the 1950s, making five bumps in 1951 and four in 1952 to reach the first division, with a high point of seventh in 1958. It later returned to the second division, before re-entering the first division in 1970. Its highest position in recent years was seventh in the first division in 2000 and in 2001; it has been back in the second division since 2004. Women were first admitted to Jesus College in 1974, when the college was one of the first five men's colleges to become co-educational. The college women's 1st VIII reached a high point of second in the first division of Eights Week in 1983, but have been in the third division since 2002. The women's 1st VIII won their "blades" in both Torpids and Eights Week in 1993, an achievement that led to the crew being described by the editor of the Jesus College Record as vying "not just for the College team of the decade, but perhaps for the team of the last three decades", in any sport.
D. W. Griffith, the stroke of the Jesus College boat, was present at the inaugural meeting of the Oxford University Boat Club on 23 April 1839. However, Jesus College oarsmen played an infrequent part in university rowing in the nineteenth century. No Jesus College student served on the OUBC committee between 1839 and 1899, the last year for which Sherwood gives records. Two students from the college (W. S. Thompson and E. W. Davies (cox)) were part of the losing Oxford crew in the second Oxford-Cambridge boat race in 1836. Between 1858 and 1899, seven others trialled, unsuccessfully, for places in the Oxford University crew. Since then, college representation in the Boat Race has been more frequent: M. L. Thomas and D. R. Glynne Jones (1952); Boris Mavra (1992, 1993 and 1995); the Canadian 2004 Olympic rowing silver medallist Barney Williams (2005 and 2006); and Brodie Buckland (2007). Various women have won their "Blue" for competing in the Women's Boat Race against Cambridge: Anna Bean and Ann Bevitt (1989); Louise Sanford (1997); and Claire Weaver (1998).
Some prominent individuals rowed whilst they were students at the college. The historian Albert Pollard was Captain of Boats in 1890, having rowed in the boat that was last on the river in 1889. Alwyn Williams (later Bishop of Durham), who was at the college from 1906 to 1911, was also boat club captain. Maurice Jones (later Principal of St David's College, Lampeter) was a cox. John Sankey (later Lord Chancellor) rowed in a Torpid boat that went down four places. The baritone David Ffrangcon Davies rowed in a boat that went up five places in Torpids and four in Eights Week. Angus Buchanan, who won the Victoria Cross in 1916 during the First World War, rowed in a college four in 1919, despite having been blinded in 1917. Anton Muttukumaru (later Commander of the Ceylon Army) rowed at bow in a college four.
Colleges began to keep barges moored on the side of the river on Christ Church Meadow from 1839; these would be used for crews to change, for spectators to watch the races and for social functions. Jesus shared a barge with New, St John's and Pembroke after 1857. In 1911, Jesus purchased their own barge from Salters, at a cost of £940.14s.8d. It had previously been owned by one of the Livery Companies of the City of London and had been used in the days when the Lord Mayor's Show took place on the River Thames in London rather than through the streets. It sank in 1955, but was salvaged and restored. It was replaced by the college's boathouse in 1964 (which is shared with the boat club of Keble College), and moved to Maidenhead where it was later restored. It returned to Oxford in 1987, but was badly damaged by fire in January 1988. It was again restored (decorated in the college colours of green and white, and with a Welsh red dragon still on the prow) and moved to Richmond-upon-Thames, where it is moored alongside Richmond Bridge and used as a restaurant.