Several ducted fuel injection (DFI) studies have highlighted the importance of accuracy in aligning the duct axis with that of its corresponding spray for optimal effectiveness, as misalignment adversely impacts the method’s performance. The need for accurate alignment could lead to added manufacturing complexity via tighter tolerances. This study systematically explores cases of horizontal, vertical, and rotational misalignment, analyzing their respective effects on DFI performance. Vertical and horizontal misalignments at the duct inlet plane were varied at magnitudes of 6.25%, 12.5%, and 25.0% of the duct diameter, corresponding to 0.125, 0.25, and 0.5 mm, respectively. Rotational misalignments were set at 1°, 2°, and 4°, corresponding to 3.65%, 7.30%, and 14.6%, respectively, of the duct diameter at its inlet plane. The investigation yields spray-duct alignment tolerance limits and highlights the influence of misalignment direction on emissions due to the interactions with swirl and squish inside the combustion chamber. The results indicate that the tolerance limits for the alignment are within 4° and 0.5 mm relative to the geometrically aligned position. If the misalignment exceeds 4°of rotation or 0.5 mm in the horizontal direction, the beneficial effects on soot reduction using this method are no longer observed. The findings contribute to an understanding that can be used to optimize DFI for cleaner and more efficient combustion in compression-ignition engines.