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Background: Currently, phacoemulsification is a very common cataract surgical procedure in which the lens is emulsified and aspirated from the eye through a small corneal incision. Aim: To compare early regional corneal thickness changes following phacoemulsification done by experienced surgeons versus trainee surgeons. Setting: A prospective cohort study was done at Ibn Al Haitham tertiary eye hospital in Baghdad, Iraq. Methods: The data were collected for 5 months, from 01 March 2018 until 31 July 2018. Adult patients undergoing phacoemulsification and intraocular lens surgery were prospectively evaluated and divided into two groups. Group 1 comprised those operated by experienced surgeons, whilst Group 2 patients were operated by trainee surgeons. Slit lamp examination and endothelial specular microscopy were assessed with the measurement of central corneal thickness (CCT) and peripheral corneal thickness (PCT), using Scheimpflug imaging (Pentacam). Results: There was a significant statistical difference in post-operative CCT between Groups 1 and 2, being 596.72 ± 50.69 µ m compared to 631.54 ± 67.84 µ m in Groups 1 and 2, respectively, with a mean difference of 34.82 µ m ( p = 0.000). More difference was observed in post-operative PCT (148.38 µ m) as it was 734.8 ± 88.55 µ m in the experienced group, compared to 883.18 ± 128.43 µ m in the trainee group ( p = 0.005). Conclusion: Phacoemulsification done by trainee surgeons was associated with higher CCT and PCT.