Emitter clogging in drip irrigation, caused by poor water quality and inadequate system operating pressure, can affect distribution uniformity of emitters and may cause inadequate irrigation applications. The objective of this study was to evaluate efficiency of different concentrations and schedules of chlorination to clean emitters for improving distribution uniformity. This study was conducted on drip irrigation system, installed in citrus orchard at experimental area of Water Management Research Centre, University of Agriculture, Faisalabad. The physical and chemical analysis along with bacteriological counts were carried out for water source of particular drip irrigation system. The results showed that water has biologically severe potential to clog emitters, and consequently partial clogging of emitters was apparent due to presence of sticky bacteria layers and in field performance of particular drip irrigation system was suboptimal in terms of selected performance parameters. To improve the said system performance, five concentrations of sodium hypochlorite (i.e. C1: 30 ppm, C2: 60 ppm, C3: 100 ppm, C4: 150 ppm, C5: 200 ppm) and three schedules (S1: five times/month, S2: three times/month and S3: two times/month) were used for chlorination process. The comparative analysis indicated that after application of treatments, performance parameters such as coefficient of variation (Cv), emission uniformity (Eu) and statistical uniformity ( Us) were improved from 0.221 to 0.097, 61.30 to 82.0% and 77.90 to 90.30%, respectively. The statistical analysis further showed that treatments with C1: 30 ppm and C2: 60 ppm were not effective to achieve the required performance targets. While, the treatments with C3: 100 ppm, C4: 150 ppm and C5: 200 ppm showed the best performance in the order of S1: five times/month, S2: three times/month and S3: two times/month, respectively.