We investigated how the abnormalities of fixation eye movements (FEMs) of the amblyopic eye were linked with treatment outcomes following part-time patching therapy in children with amblyopia. Methods We recruited 53 patients, with at least 12 months of patching, and measured FEMs at the end of treatment. Subjects were classified based on FEM waveforms (those without nystagmus = 21, those with nystagmus without fusion maldevelopment nystagmus (FMN) = 21, and those with FMN = 11) and based on clinical type of amblyopia (anisometropic = 18, strabismic = 6, and mixed = 29). The treatment outcomes such as duration of treatment of receiving part-time patching therapy, visual acuity and stereo-acuity deficits at the end of treatment were determined. Bivariate contour ellipse area (BCEA), fast (fixational saccade/ quick phases), and slow (inter-saccadic drifts/slow phases) FEMs of the fellow and amblyopic eye were analyzed. Results Anisometropic group had less residual amblyopia (0.23±0.19logMAR acuity) compared to strabismic/mixed (0.36±0.26) groups (p = 0.007). Treatment duration in patients without nystagmus was lower (12.6±9.5months) compared to nystagmus without FMN (25.6±23.2) and FMN (29.5±20.4) groups (p = 0.006). Patients without nystagmus had better stereopsis at the end of treatment (2.3±0.84logarcsecs) compared to nystagmus without FMN (2.6