This study explores the sensitivity of jump type (unilateral and bilateral) and output variable (mean force, propulsive impulse, and jump height) to detect the changes in inter-limb asymmetries induced by unilateral and bilateral fatigue protocols. Thirty-eight individuals performed two testing sessions that consisted of (I) nine “pre-fatigued” countermovement jumps (CMJs; three bilateral and six unilateral [three with each leg]), (II) fatigue protocol and (III) nine “post-fatigued” CMJs. The testing sessions only differed in the fatigue protocol (five sets to failure against the 15-repetition maximum load using either the unilateral or bilateral knee extension exercise). The magnitude of all CMJ-derived variables (mean force, impulse, and jump height) decreased following both unilateral (p ≤ 0.002) and bilateral fatigue protocols (p ≤ 0.018). However, only unilateral protocol accentuated inter-limb asymmetries, which was detected for all variables during the unilateral CMJ (from −4.33% to −2.04%; all p < 0.05) but not during the bilateral CMJ (from −0.64% to 0.54%; all p > 0.05). The changes in inter-limb asymmetries following the unilateral and bilateral fatigue protocols were not significantly correlated between the unilateral and bilateral CMJs (rs ≤ 0.172). The unilateral CMJ should be recommended for the testing purposes over the bilateral CMJ due to its greater sensitivity to detect the selective effects of fatigue.