Marion Barber has scored the most career rushing touchdowns when rushing for <5,000 yards, with 53 touchdowns.

most career rushing touchdowns with less than 5000 rushing yards
Interpreted as:
most career rushing touchdowns by a player with less than 5000 rushing yards
BarberBellHornungBanaszakHaynesMatteKamaraDuckettKinnebrewYoungTowlerGreen-EllisHectorAndersonJonesWheatleyOkoyeBrownMcCauleyJohnsonKempSmithAmeche5351504746454444444343424141404040404040404040
NAMEGPRUSH TDRUSH YDSATTYPCRUSH YDS/GREC YDSRECTRGAVGREC YDS/GREC TD
Marion BarberMarion Barber99534,7801,1564.148.31,3301792327.413.46
Greg BellGreg Bell80514,9591,2044.162.01,3071578.316.37
Paul HornungPaul Hornung104503,7118934.235.71,48013011.414.212
Pete BanaszakPete Banaszak173473,7729643.921.81,0221218.45.95
Abner HaynesAbner Haynes112464,6301,0364.541.33,53528712.331.620
Tom MatteTom Matte142454,6461,2003.932.72,86924911.520.212
Alvin KamaraAlvin Kamara66443,7597864.857.03,0653514428.746.419
T.J. DuckettT.J. Duckett93442,8147173.930.330335448.73.30
Larry KinnebrewLarry Kinnebrew88443,1337794.035.6660709.47.53
Steve YoungSteve Young169434,2397225.925.12201.00.00
Dan TowlerDan Towler67433,4936725.252.16656210.79.91
BenJarvus Green-EllisBenJarvus Green-Ellis84423,9141,0083.946.641852778.05.00
Johnny HectorJohnny Hector126414,2801,0514.134.01,6611888.813.23
Donny AndersonDonny Anderson126414,6961,1973.937.32,54820912.220.214
Aaron JonesAaron Jones62403,8277555.161.71,2941642237.920.910
Tyrone WheatleyTyrone Wheatley124404,9621,2703.940.09001251417.27.37
Christian OkoyeChristian Okoye79404,8971,2463.962.0294427.03.70
Ted BrownTed Brown104404,5461,1174.143.72,8503398.427.413
Don McCauleyDon McCauley156402,6277703.416.83,0263339.119.417
Ron JohnsonRon Johnson81404,3081,2043.653.21,9772139.324.415
Jack KempJack Kemp122401,1503563.29.4-91-9.0-0.10
J.D. SmithJ.D. Smith131404,6721,1004.235.71,1221278.88.66
Alan AmecheAlan Ameche70404,0459644.257.87331017.310.54
David JohnsonDavid Johnson81393,9239554.148.42,68726037910.333.218
Joseph AddaiJoseph Addai78394,4531,0954.157.11,4481912497.618.69
StatMuse has season-level data for rushing yards going back to the 1932 season.