Phyllanthus amarus Schum. & Thonn. belongs to the family Euphorbiaceae, commonly known as “Bhooamalakee” or “Bhuti”, traditionally being used for the treatment of gastrointestinal troubles, kidney, liver problems, etc. In the present study, a validated high-performance thin-layer chromatography method was established for the estimation of two bioactive lignans, phyllanthin and hypophyllanthin, in the ethanolic extracts of P. amarus with the aim to see the effect of seasons on the quantity of the aforesaid phytoconstituents. The plant material was collected in July, August, September and October months during 2017–2018 from Lucknow, India. The method was validated in terms of precision, repeatability, specificity, sensitivity linearity and robustness. The method permits reliable quantification and showed good resolution on silica gel with toluene‒ethyl acetate (8.5:1.5, V/V) as the mobile phase, and characteristic bands of phyllanthin and hypophyllanthin were observed at RF 0.21, and 0.35, respectively. The level of quantified lignans varies in different months. Our finding indicated that the month of August may be appropriate for the collection of P. amarus for the preparation of therapeutic formulations because of the optimal level of both phyllanthin and hypophyllanthin, known for together work in the treatment of liver necrosis, carcinomas and asthma, etc.