Squamous cell carcinoma of kidney is extremely rare tumor and the incidence is less than 1% of all renal malignancies. In the world literature till now, very few cases of primary squamous cell carcinoma of kidney have been reported. Squamous cell carcinoma is frequently associated with renal calculi and hydronephrosis. Squamous cell carcinoma of kidney is very aggressive, presents at an advanced stage and is associated with poor prognosis. Here, we report a case of squamous cell carcinoma diagnosed in hydronephrotic kidney with multiple renal calculi in a 60 year old male patient. Patients presenting with long standing history of renal calculus and associated hydronephrosis should undergo extensive diagnostic workup for the early diagnosis of squamous cell carcinoma, so that we can reduce the morbidity and mortality.