Background Acrylamide (AA) is an industrial monomer which is used in many industries. Dietary or occupational exposure affects high percentage of population. It causes multi-organ toxicity including neurotoxicity, hepatotoxicity and nephrotoxicity via induction of oxidative stress and inflammation. AA induced nephrotoxicity is a major health problem that needs our concern. Berberine (BBR) is an alkaloid that has nephroprotective effects as being an antioxidant and an anti-inflammatory. Aim The aim of this work was to shed light on autophagy and nucleotide binding oligomerization domain like receptor family pyrin domain containing 3 (NLRP3) inflammasome formation and to assess the ameliorating effect of BBR as antioxidant, anti-inflammatory and autophagy modulator on experimental model of AA induced nephrotoxicity. Materials and methods This study was done on 50 male rats, which were randomly divided equally into 5 groups: control group; Acrylamide group (received AA only); Berberine-Acrylamide co-treatment group (received AA and BBR simultaneously); prophylaxis group (given BBR alone for 10 days followed by BBR and AA for another 10 days); and Berberine group (received BBR only). Results Administration of BBR as a prophylactic agent enhanced kidney function, restored electrolyte balance, suppressed oxidative stress and NLRP3 inflammasome and induced mitophagy. However, its administration as a co-treatment with AA showed ameliorating effect. The histopathological changes were consistent with the biochemical results. Conclusion: BBR could protect against AA induced nephrotoxicity through reduction of oxidative stress, suppression of NLRP3 inflammasome and induction of mitophagy. The usage of BBR as a protective drug against the progression of nephrotoxicity seems to be promising.