| May 2004 | Tornado (F2) | Jacksonville | 1 hurt, $4,000,000 | A small tornado touched down in the southwest section of Jacksonville near the point where Route 67 turns north. As it traveled to the northeast it quickly intensified to F2 strength destroying a furniture store, house and church and caused major damage to a motel. One occupant of the motel sustained minor injuries. The tornado then quickly weakened causing minor damage to several more homes and businesses before lifting and dissipating. |
| April 1996 | Tornado (F2) | Jacksonville | 1 hurt, $400,000 | no account filed |
| May 2004 | Thunderstorm Wind | Jacksonville | $1,000,000 | Thunderstorm winds caused a large swath of damage across town. Numerous trees, tree limbs and power lines were blown down. Also, several homes sustained minor roof damage. The county courthouse also sustained roof damage. No injuries were reported. |
| June 2014 | Thunderstorm Wind | Jacksonville | $120,000 | A roof was blown off a building at 665 S. West Street. Minor roof damage was reported to 12 houses and 2 garages. Numerous tree branches were blown down from the corner of Lincoln and Morton to College, then east to Clay and south to Morton. Several trees and power lines were blown down around town. |
| December 2002 | Thunderstorm Wind | Jacksonville | $100,000 | no account filed |
| August 2010 | Thunderstorm Wind | Jacksonville | $45,000 | Numerous tree limbs were blown down across Jacksonville. A tree was snapped at the trunk and fell onto Hoagland Boulevard. A large window at a bridal shop was broken and several homes lost shingles from their roofs. |
| September 2008 | Flash Flood | Jacksonville | $35,000 | The basement at Westfair Christian Academy in Jacksonville was flooded. |
| June 2009 | Thunderstorm Wind | Jacksonville | $30,000 | Numerous trees and tree limbs were blown down around the city of Jacksonville. |
| July 2015 | Thunderstorm Wind | Jacksonville | $25,000 | A few power poles were blown down on the south side of Jacksonville. |
| July 2008 | Thunderstorm Wind | Jacksonville | $25,000 | Numerous trees and power lines were blown down in Jacksonville. |
| June 2015 | Thunderstorm Wind | Jacksonville | $20,000 | Several trees were blown down. |
| May 2009 | Thunderstorm Wind | Jacksonville | $20,000 | Several trees were blown down on the south side of Jacksonville. |
| August 2009 | Thunderstorm Wind | Jacksonville | $20,000 | Numerous power lines were blown down in Jacksonville. |
| May 2021 | Thunderstorm Wind | Jacksonville | $15,000 | A few trees and power lines were blown down. |
| July 2015 | Thunderstorm Wind | Jacksonville | $15,000 | Several large tree limbs were knocked down and shingles were blown across the road on South Westgate Avenue. |
| September 2012 | Thunderstorm Wind | Jacksonville | $15,000 | Several 2-inch diameter tree branches were blown down. |
| May 2011 | Thunderstorm Wind | Jacksonville | $15,000 | Several large tree limbs were blown down in Jacksonville. |
| August 2008 | Thunderstorm Wind | Jacksonville | $15,000 | Several two-foot diameter trees were blown down. Power lines were blown down and blocked Highway 104. |
| May 2011 | Thunderstorm Wind | Jacksonville | $10,000 | The tops of several 8 to 10-inch diameter trees were snapped off near 67 and Old 36 just west of Jacksonville. |
| July 2010 | Thunderstorm Wind | Jacksonville | $7,000 | A tree and powerline were blown down 1 mile north of Jacksonville. |
| May 1998 | Thunderstorm Wind | Jacksonville | $6,000 | As a thunderstorm moved east across Morgan County its winds blew down several trees and power lines in Jacksonville and one mile east of Alexander. Also, the winds caused minor damage to the roof of a livestock building at the Morgan County Fairgrounds in Jacksonville. No injuries were reported. |
| August 2008 | Thunderstorm Wind | Jacksonville | $5,000 | Eight-inch diameter limbs were blown down onto a house. |
| August 2008 | Thunderstorm Wind | Jacksonville | $5,000 | A power pole was blown down onto a house in South Jacksonville. |
| June 2018 | Thunderstorm Wind | Jacksonville | $4,000 | Two large trees were blown down in Jacksonville, including one that fell on a fence. |
| July 2016 | Thunderstorm Wind | Jacksonville | $1,000 | A large tree branch was blown down on the west side of Jacksonville. |
| June 2025 | Tornado (EF1) | Jacksonville | - | A tornado began near State Highway 104, between Lafayette Avenue and Westwinds Drive. It tracked northeast for 3.6 miles and was on the ground for eight minutes, with the most prolific damage being rated EF-1. The tornado damaged numerous trees, a power company outbuilding, and caused roofing damage to multiple residences on the northwest side of Jacksonville. It then struck an outdoor sports complex, causing substantial damage to the middle portion of an outbuilding, shredding outdoor baseball netting, and strewing sheet metal and other debris to the northeast through the fields. The tornado continued through open fields for several miles before producing additional damage to trees, outbuildings, and residences along Baldwin and Sandusky Roads, immediately southwest of the Jacksonville Airport. It continued northeast through the northwest corner of the Jacksonville Airport property before damaging some trees along Zimmer Road and lifting. |
| June 2025 | Thunderstorm Wind | Jacksonville | - | A softwood tree was snapped. |
| September 2025 | Thunderstorm Wind | Jacksonville | - | A tree was blown onto a house and 4 other trees were knocked down across roadways in Jacksonville. |
| June 2023 | Thunderstorm Wind | Jacksonville | - | A tree was blown onto a truck. |
| June 2023 | Thunderstorm Wind | Jacksonville | - | A large tree was snapped about halfway up the trunk. |
| June 2023 | Thunderstorm Wind | Jacksonville | - | Numerous tree branches were blown down across Jacksonville. |
| June 2023 | Thunderstorm Wind | Jacksonville | - | Numerous tree branches were blown down. |
| May 2022 | Thunderstorm Wind | Jacksonville | - | A large tree and numerous tree branches were blown down across Jacksonville. |
| September 2022 | Hail | Jacksonville | - | Golf ball-sized hail lasted 15 minutes and shredded leaves. |
| September 2022 | Thunderstorm Wind | Jacksonville | - | Multiple large trees were blown down across Jacksonville, some of which were over a foot in diameter. |
| September 2022 | Thunderstorm Wind | Jacksonville | - | Several large trees were blown over. |
| October 2021 | Thunderstorm Wind | Jacksonville | - | Damage was reported along the length of Vandalia Road on the south side of Jacksonville. Numerous trees and power lines were blown down and the facade was torn off a church. |
| June 2019 | Thunderstorm Wind | Jacksonville | - | Power lines were blown down in Jacksonville. |
| May 2019 | Flood | Jacksonville | - | Heavy rainfall of 2.00 to 4.00 inches during the morning resulted in a large area of flooding in eastern Morgan County, including the city of Jacksonville. Numerous rural roads in the county, and streets in Jacksonville were flooded. Illinois Route 78 two miles north of Jacksonville was impassable due to water flowing over the roads. |
| June 2018 | Thunderstorm Wind | Jacksonville | - | A power line was blown down. |
| August 2011 | Hail | Jacksonville | - | Hail ranged from pea sized to half-dollar sized. |
| May 2006 | Thunderstorm Wind | Jacksonville | - | Several trees and power lines were blown down. |
| July 2006 | Thunderstorm Wind | Jacksonville | - | Numerous trees and power lines were blown down. |
| July 2006 | Thunderstorm Wind | Jacksonville | - | Numerous trees and tree limbs were blown down. Also, a section of bleachers was destroyed at a little league baseball field. |
| January 2005 | Flash Flood | Jacksonville | - | Numerous streets were flooded in town. |
| August 2005 | Thunderstorm Wind | Jacksonville | - | A few trees blown down. |
| September 2005 | Thunderstorm Wind | Jacksonville | - | A few tree limbs blown down. |
| November 2005 | Thunderstorm Wind | Jacksonville | - | Power lines blown down. |
| August 2004 | Flash Flood | Jacksonville | - | Several city streets were flooded due to heavy rains. |
| April 2003 | Thunderstorm Wind | Jacksonville | - | A large tree was blown down on the north side of town. |
| August 2002 | Thunderstorm Wind | Jacksonville | - | Several trees were blown down. |
| July 2000 | Thunderstorm Wind | Jacksonville | - | Several trees were blown down in Jacksonville. Also, several power lines were blown down in Jacksonville and Waverly. |
| April 1999 | Thunderstorm Wind | Jacksonville | - | Thunderstorm winds blew down ten power poles in Jacksonville and caused minor damage to a couple of homes in town. No injuries were reported. |
| April 1999 | Tornado (F1) | Jacksonville | - | A tornado touched down 5.5 miles west of Jacksonville. It threw a boat off its trailer a quarter of a mile into a neighbor's pond. A house nearby sustained some shingle and window damage and a truck was damaged. As the tornado travelled to the northeast, it blew down dozens of trees and destroyed a barn. Nearby the roof of an airplane hanger was peeled back with the sheet metal thrown into trees. A 2x4 was driven into the southwest side of a house. After the tornado crossed Route 67, it continued to the northeast knocking down trees and power poles. In Arcadia, a barn was severely damaged, several outbuildings were destroyed, a garage was damaged, and roof damage was reported to several homes before the tornado lifted and dissipated. No injuries were reported. |
| April 1997 | Thunderstorm Wind | Jacksonville | - | In Jacksonville, the thunderstorm winds damaged the tin roof of a trailer home, though no injuries were reported. |
| May 2025 | Hail | Jacksonville | - | no account filed |
| May 2025 | Hail | Jacksonville | - | no account filed |
| May 2025 | Hail | Jacksonville | - | no account filed |
| May 2025 | Thunderstorm Wind | Jacksonville | - | no account filed |
| March 2023 | Hail | Jacksonville | - | no account filed |
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