Discoveries 

Sheppard was the lead discoverer of the object with the most distant orbit known in the Solar System,  (nicknamed Biden). In 2014, the similarity of the orbit of  to other extreme Kuiper belt object orbits led Sheppard and Trujillo to propose that an unknown :en:Super-Earth mass planet (2–15 Earth masses) in the outermost Solar System beyond 200 AU and up to 1500 AU is shepherding these smaller bodies into similar orbits (see :en:Planet X or :en:Planet Nine). The extreme trans-Neptunian objects  and , announced in 2016 and co-discovered by Sheppard, further show a likely unknown massive planet exists beyond a few hundred AU in the Solar System, with  being the first known high semi-major axis and high perihelion object anti-aligned with the other known extreme objects. In 2018, the announcement of the high perihelion inner Oort cloud object :en:541132 Leleākūhonua (nicknamed "The Goblin") by Sheppard et al., being only the third known after  and Sedna, further demonstrated that a super-Earth planet in the distant solar system likely exists as Leleākūhonua has many orbital similarities as the two other known inner Oort cloud objects.

Most notable discoveries 

Sheppard has been involved in the discovery of many small Solar System bodies such as trans-Neptunian objects, centaurs, comets and near-Earth objects.
 Three comets are named after him which are Sheppard-Trujillo (C/2014 F3), Sheppard-Tholen (C/2015 T5) and comet Trujillo-Sheppard (P/2018 V5).
 The possible dwarf planets discovered by Sheppard are 471143 Dziewanna, , , ,  and .
 In 2018, Sheppard was the lead discoverer of the most distant observed object in our solar system and first object observed beyond 100 AU, dwarf planet  (nicknamed Farout), which is around 120 AU from the Sun.
 He discovered a minor-planet moon around likely dwarf planet .
 He is also a co-discoverer of a minor-planet moon orbiting the binary trans-Neptunian object 341520 Mors–Somnus.<ref name="circ8962" />
 Among the numerous irregular moons of the major planets in whose discovery he has been involved are:<ref name="jpl-Satellite-Discovery-Circumstances" />

Jupiter
Discovered moons of Jupiter (full list):<ref name="jpl-Satellite-Discovery-Circumstances" />

 Themisto (2000), first seen but lost in 1975 by Charles Kowal
 Harpalyke (2000)
 Praxidike (2000)
 Chaldene (2000)
 Isonoe (2000)
 Erinome (2000)
 Taygete (2000)
 Kalyke (2000)
 Megaclite (2000)
 Iocaste (2000)
 Dia (2000)
 Euporie (2001)
 Orthosie (2001)
 Euanthe (2001)
 Thyone (2001)
 Hermippe (2001)
 Pasithee (2001)
 Aitne (2001)
 Eurydome (2001)
 Autonoe (2001)
 Sponde (2001)
 Kale (2001)
 Arche (2002)
 Eukelade (2003)
 Helike (2003)
 Aoede (2003)
 Hegemone (2003)
 Kallichore (2003)
 Cyllene (2003)
 Mneme (2003)
 Thelxinoe (2003)
 Carpo (2003)
 Kore (2003)
 Herse (2003)
 S/2003 J 2 (2003)
 Eupheme (2003)
 S/2003 J 4 (2003)
 Eirene (2003)
 S/2003 J 9 (2003)
 S/2003 J 10 (2003)
 S/2003 J 12 (2003)
 Philophrosyne (2003)
 S/2003 J 16 (2003)
 Jupiter LV (2003)
 Jupiter LXI (2003)
 S/2003 J 23 (2003)
 S/2003 J 24 (2003)
 Jupiter LXXII (2011)
 Jupiter LVI (2011)
 S/2011 J 3 (2011)
 Jupiter LIV (2016)
 Valetudo (2016)
 S/2016 J 3 (2016)
 Jupiter LIX (2017)
 Jupiter LXIII (2017)
 Jupiter LXIV (2017)
 Pandia (2017)
 Jupiter LXVI (2017)
 Jupiter LXVII (2017)
 Jupiter LXVIII (2017)
 Jupiter LXIX (2017)
 Jupiter LXX (2017)
 Ersa (2018)
 S/2018 J 2 (2018)
 S/2021 J 1 (2021)

Saturn
Discovered moons of Saturn (full list):<ref name="jpl-Satellite-Discovery-Circumstances" />

 Narvi (2003)
 Fornjot (2004)
 Farbauti (2004)
 Aegir (2004)
 Bebhionn (2004)
 Hati (2004)
 Bergelmir (2004)
 Fenrir (2004)
 Bestla (2004)
 Kari (2004)
 S/2004 S 7 (2004)
 S/2004 S 12 (2004)
 S/2004 S 13 (2004)
 S/2004 S 17 (2004)
 Hyrrokkin (2006)
 Loge (2006)
 Surtur (2006)
 Skoll (2006)
 Greip (2006)
 Jarnsaxa (2006)
 S/2006 S 1 (2006)
 S/2006 S 3 (2006)
 Tarqeq (2007)
 S/2007 S 2 (2007)
 S/2007 S 3 (2007)
 Gridr (2019)
 S/2004 S 21 (2019)
 Angrboda (2019)
 Skrymir (2019)
 S/2004 S 24 (2019)
 Gerd (2019)
 Saturn LVIII (2019)
 Eggther (2019)
 S/2004 S 28 (2019)
 Saturn LX (2019)
 Beli (2019)
 S/2004 S 31 (2019)
 Gunnlod (2019)
 Thiazzi (2019)
 Saturn LXIV (2019)
 Alvaldi (2019)
 S/2004 S 36 (2019)
 S/2004 S 37 (2019)
 Geirrod (2019)
 S/2004 S 39 (2019)

 Uranus
Discovered moons of Uranus (full list):<ref name="jpl-Satellite-Discovery-Circumstances" />
 Margaret (2003)
 Ferdinand (2003), first seen but lost in 2001 by Holman et al.

 Neptune
Discovered :en:moons of Neptune (full list):<ref name="jpl-Satellite-Discovery-Circumstances" />
 Psamathe (2003)

Discoveries