| Either Way | Sky Blue Sky | 160 | 10.0% | 12.6 | Mar 6, 2006 | Jul 11, 2026 | Rare |
| Hell Is Chrome | A Ghost Is Born | 158 | 9.9% | 4.6 | May 19, 2004 | Dec 13, 2024 | Rare |
| It's Just That Simple | A.M. | 158 | 9.8% | 14.3 | Apr 28, 1995 | Jul 11, 2026 | Rare |
| Far, Far Away | Being There | 157 | 9.7% | 12.8 | May 19, 1996 | Dec 5, 2024 | Rare |
| Evicted | Cousin | 142 | 8.9% | 8.1 | Aug 22, 2023 | Jul 11, 2026 | Rare |
| Shouldn't Be Ashamed | A.M. | 139 | 8.6% | 8.3 | Nov 17, 1994 | Jul 9, 2026 | Rare |
| We've Been Had | Anodyne | 137 | 8.6% | 17.5 | Nov 17, 1994 | Nov 17, 2017 | Rare |
| I Am My Mother | Cruel Country | 136 | 8.4% | 3.8 | May 27, 2022 | Jun 16, 2025 | Rare |
| Everyone Hides | Ode to Joy | 135 | 8.4% | 14.6 | Sep 4, 2019 | Jul 11, 2026 | Rare |
| Christ For President | Mermaid Avenue | 133 | 8.3% | 12.8 | Dec 31, 1997 | Jul 7, 2026 | Rare |
| Pickled Ginger | Star Wars | 126 | 7.9% | 6.9 | Jul 8, 2015 | Nov 17, 2017 | Rare |
| That's Not The Issue | A.M. | 119 | 7.4% | 7 | Nov 17, 1994 | Jan 19, 2020 | Rare |
| Someone Else's Song | Being There | 115 | 7.2% | 8.9 | Sep 8, 1996 | Jan 15, 2026 | Rare |
| The Lonely 1 | Being There | 114 | 7.1% | 19 | Oct 8, 1995 | Apr 6, 2023 | Rare |
| Pick Up The Change | A.M. | 113 | 7.0% | 8.4 | Nov 17, 1994 | Aug 25, 2025 | Rare |
| One By One | Mermaid Avenue | 109 | 6.8% | 10.2 | Sep 23, 2001 | Jun 26, 2026 | Rare |
| Someday Soon | Being There | 108 | 6.6% | 8 | May 19, 1996 | Aug 25, 2025 | Rare |
| The Joke Explained | Star Wars | 103 | 6.4% | 4.4 | Jul 8, 2015 | Dec 5, 2023 | Rare |
| Outta Mind (Outta Sight) | Being There | 100 | 6.2% | 20.5 | Dec 23, 1994 | Apr 25, 2025 | Rare |
| Too Far Apart | A.M. | 100 | 6.2% | 11.8 | Nov 17, 1994 | Jan 17, 2026 | Rare |
| Remember The Mountain Bed | Mermaid Avenue, Vol. 2 | 99 | 6.2% | 6.5 | Jan 9, 2000 | Jun 26, 2026 | Rare |
| Someone to Lose | Schmilco | 98 | 6.1% | 9.3 | Aug 30, 2016 | Dec 11, 2024 | Rare |
| Wilco (The Song) | Wilco (the album) | 96 | 6.0% | 3.5 | Apr 14, 2009 | Jun 28, 2024 | Rare |
| Not For The Season | | 94 | 5.9% | 11.5 | Mar 11, 2002 | Sep 4, 2003 | Rare |
| Nothing'severgonnastandinmyway(again) | Summerteeth | 89 | 5.6% | 9.2 | Apr 14, 1999 | Jan 18, 2026 | Rare |
| One Sunday Morning (Song For Jane Smiley's Boyfriend) | The Whole Love | 89 | 5.6% | 2.6 | Sep 17, 2011 | Aug 29, 2025 | Rare |
| Why Would You Wanna Live | Being There | 88 | 5.5% | 8.5 | Nov 13, 1996 | Jun 23, 2017 | Rare |
| One and a Half Stars | Ode to Joy | 87 | 5.4% | 5.9 | Sep 4, 2019 | Apr 29, 2023 | Rare |
| Laminated Cat | Loose Fur | 86 | 5.4% | 11.9 | Mar 23, 2010 | Dec 14, 2024 | Rare |
| Candyfloss | Summerteeth | 84 | 5.2% | 15.6 | Nov 1, 1997 | Jul 1, 2026 | Rare |
| Cold Slope | Star Wars | 82 | 5.1% | 9.6 | Jul 8, 2015 | Jan 17, 2026 | Rare |
| Cry All Day | Schmilco | 82 | 5.1% | 3.4 | Aug 31, 2016 | Dec 2, 2023 | Rare |
| You Never Know | Wilco (the album) | 82 | 5.1% | 19.2 | May 26, 2009 | Jun 19, 2025 | Rare |
| Annihilation | Hot Sun Cool Shroud | 81 | 5.1% | 17.2 | Jun 29, 2024 | Jul 11, 2026 | Rare |
| Summer Teeth | Summerteeth | 81 | 5.0% | 10.1 | Jun 12, 1998 | Jul 3, 2024 | Rare |
| A Magazine Called Sunset | More Like The Moon EP | 80 | 5.0% | 15.4 | Sep 6, 2003 | Jan 15, 2026 | Rare |
| Story to Tell | Cruel Country | 80 | 5.0% | 6.6 | May 27, 2022 | Apr 30, 2026 | Rare |
| Less Than You Think | A Ghost Is Born | 79 | 4.9% | 8.4 | Aug 31, 2002 | Jun 22, 2025 | Rare |
| King of You | Star Wars | 78 | 4.9% | 10.3 | Jul 8, 2015 | Jan 17, 2026 | Rare |
| The Long Cut | Anodyne | 77 | 4.8% | 11.8 | Nov 17, 1994 | Jul 31, 2000 | Rare |
| Wishful Thinking | A Ghost Is Born | 77 | 4.8% | 7.2 | May 19, 2004 | May 5, 2026 | Rare |
| Sky Blue Sky | Sky Blue Sky | 76 | 4.7% | 9.7 | Apr 16, 2007 | Jan 15, 2026 | Rare |
| I'll Fight | Wilco (the album) | 75 | 4.7% | 9.4 | Oct 25, 2008 | May 30, 2025 | Rare |
| Locator | Schmilco | 72 | 4.5% | 18.7 | Aug 14, 2016 | Jun 15, 2019 | Rare |
| Should've Been In Love | A.M. | 70 | 4.4% | 9.2 | Nov 17, 1994 | Apr 25, 2025 | Rare |
| You And I | Wilco (the album) | 70 | 4.4% | 13.8 | Jun 25, 2009 | Jun 27, 2026 | Rare |
| Bright Leaves | Ode to Joy | 68 | 4.2% | 1.1 | Sep 4, 2019 | Dec 2, 2023 | Rare |
| More... | Star Wars | 67 | 4.2% | 1.3 | Jul 8, 2015 | Sep 10, 2016 | Rare |
| Give Back The Key To My Heart [Doug Sahm] | Anodyne | 63 | 3.8% | 16.3 | Nov 17, 1994 | Dec 3, 2023 | Rare |
| Say You Miss Me | Being There | 63 | 3.9% | 11.1 | Jul 20, 1995 | Jul 11, 2026 | Rare |
| When The Roses Bloom Again | Chelsea Walls | 61 | 3.8% | 11 | Dec 31, 1997 | Jun 26, 2026 | Rare |
| Before Us | Ode to Joy | 60 | 3.7% | 2.1 | Sep 6, 2019 | Aug 22, 2021 | Rare |
| Camera | More Like The Moon EP | 60 | 3.7% | 11.2 | Apr 3, 2010 | Jan 17, 2026 | Rare |
| On And On And On | Sky Blue Sky | 60 | 3.7% | 14.2 | Sep 22, 2005 | Dec 15, 2024 | Rare |
| Kicking Television | A Ghost Is Born | 59 | 3.7% | 20.1 | Apr 21, 2003 | Jan 17, 2026 | Rare |
| What Light | Sky Blue Sky | 58 | 3.6% | 13.1 | Jul 7, 2006 | Apr 27, 2026 | Rare |
| Hold Me Anyway | Ode to Joy | 57 | 3.6% | 22.8 | Sep 7, 2019 | Aug 7, 2021 | Rare |
| Deeper Down | Wilco (the album) | 56 | 3.5% | 9.1 | Jun 20, 2009 | Jun 28, 2024 | Rare |
| White Wooden Cross | Ode to Joy | 56 | 3.5% | 9.6 | Jun 29, 2019 | Oct 6, 2021 | Rare |
| Bob Dylan's 49th Beard | More Like The Moon EP | 55 | 3.4% | 12.3 | Jul 21, 2002 | Dec 14, 2024 | Rare |
| Capitol City | The Whole Love | 53 | 3.3% | 12.5 | Sep 29, 2011 | Apr 26, 2015 | Rare |
| Sonny Feeling | Wilco (the album) | 52 | 3.2% | 12.8 | Jul 25, 2008 | Jul 1, 2026 | Rare |
| Meant to Be | Cousin | 51 | 3.2% | 10.8 | Sep 29, 2023 | Apr 27, 2026 | Rare |
| Secret Of The Sea | Mermaid Avenue, Vol. 2 | 51 | 3.2% | 8.9 | Jun 16, 2000 | Jun 26, 2026 | Rare |
| A Lifetime to Find | Cruel Country | 50 | 3.0% | 19.3 | May 27, 2022 | Mar 18, 2024 | Rare |
| Hints | Cruel Country | 50 | 3.1% | 5.1 | May 27, 2022 | May 6, 2025 | Rare |
| Standing O | The Whole Love | 49 | 3.1% | 16.9 | Jun 25, 2011 | Dec 9, 2014 | Rare |
| Where Do I Begin | Star Wars | 49 | 3.1% | 7.6 | Jul 17, 2015 | Jul 5, 2016 | Rare |
| Black Moon | The Whole Love | 46 | 2.9% | 6.8 | Sep 20, 2011 | Oct 22, 2014 | Rare |
| Gun | Still Feel Gone | 46 | 2.8% | 18.9 | Nov 21, 1994 | Nov 4, 1997 | Rare |
| Shake It Off | Sky Blue Sky | 46 | 2.9% | 7.8 | Nov 22, 2006 | Dec 9, 2014 | Rare |
| We Aren't the World (Safety Girl) | Schmilco | 46 | 2.9% | 16 | Aug 31, 2016 | Jun 28, 2019 | Rare |
| Many Worlds | Cruel Country | 45 | 2.8% | 11.5 | May 27, 2022 | Jan 15, 2026 | Rare |
| When You Wake Up Feeling Old | Summerteeth | 45 | 2.8% | 16.9 | Mar 25, 1999 | Jan 21, 2020 | Rare |
| My Darling | Summerteeth | 44 | 2.7% | 13.6 | Apr 14, 1999 | May 4, 2008 | Rare |
| Normal American Kids | Schmilco | 44 | 2.7% | 1.4 | Sep 2, 2016 | Jun 18, 2017 | Rare |
| You Satellite | Star Wars | 44 | 2.7% | 4.8 | Jul 17, 2015 | Jun 27, 2026 | Rare |
| Be Not So Fearful [Bill Fay] | Cover | 43 | 2.6% | 19.4 | Mar 19, 2002 | Apr 24, 2022 | Rare |
| We're Just Friends | Summerteeth | 42 | 2.6% | 10.9 | Feb 17, 1999 | Feb 18, 2008 | Rare |
| Cars Can't Escape | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 41 | 2.6% | 12.9 | May 23, 1999 | Mar 23, 2023 | Rare |
| Magnetized | Star Wars | 40 | 2.5% | 10.2 | Jul 17, 2015 | Jun 1, 2016 | Rare |
| Quiet Amplifier | Ode to Joy | 40 | 2.5% | 12.1 | Jun 28, 2024 | May 1, 2026 | Rare |
| Taste the Ceiling | Star Wars | 40 | 2.5% | 5.2 | Jul 17, 2015 | Jun 1, 2016 | Rare |
| Infinite Surprise | Cousin | 39 | 2.4% | 2.4 | Sep 28, 2023 | Apr 25, 2025 | Rare |
| (Was I) In Your Dreams | Being There | 38 | 2.4% | 9.4 | Oct 11, 1995 | Jun 23, 2017 | Rare |
| Cousin | Cousin | 38 | 2.4% | 10.8 | Sep 26, 2023 | Jun 22, 2024 | Rare |
| Dreamer In My Dreams | Being There | 37 | 2.3% | 23.7 | Oct 28, 1995 | Jan 15, 2026 | Rare |
| We Were Lucky | Ode to Joy | 35 | 2.2% | 15.8 | Oct 8, 2019 | Jan 19, 2020 | Rare |
| Feed Of Man | Mermaid Avenue, Vol. 2 | 34 | 2.1% | 4.8 | Apr 27, 2000 | Jun 28, 2024 | Rare |
| In A Future Age | Summerteeth | 34 | 2.1% | 12.9 | Mar 25, 1999 | Jan 20, 2022 | Rare |
| Pittsburgh | Cousin | 31 | 1.9% | 3.5 | Sep 26, 2023 | Aug 6, 2025 | Rare |
| Tired of Taking It Out on You | Cruel Country | 30 | 1.9% | 11.6 | May 27, 2022 | Jun 20, 2025 | Rare |
| Blood Of The Lamb | Mermaid Avenue, Vol. 2 | 29 | 1.8% | 6.4 | Nov 14, 1999 | Dec 12, 2014 | Rare |
| Wait Up | March 16-20, 1992 | 29 | 1.8% | 10.2 | Nov 17, 1994 | Apr 6, 2002 | Rare |
| Country Disappeared | Wilco (the album) | 28 | 1.7% | 9.3 | Oct 26, 2008 | Aug 20, 2025 | Rare |
| ELT | Summerteeth | 28 | 1.7% | 18.3 | Dec 31, 1997 | Jun 28, 2024 | Rare |
| Acuff-Rose | Anodyne | 27 | 1.7% | 21.2 | Nov 23, 1994 | Jun 22, 2007 | Rare |
| Another Man's Done Gone [Woody Guthrie] | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 27 | 1.7% | 16.7 | Jul 4, 1998 | Jun 26, 2026 | Rare |
| At My Window Sad And Lonely | Mermaid Avenue | 27 | 1.7% | 8.1 | Jul 4, 1998 | Jun 26, 2026 | Rare |
| Panthers (Proving Death Again) | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 27 | 1.7% | 9.2 | Dec 6, 2014 | Apr 25, 2025 | Rare |