The downstream effect of the pandemic on global cancer prevention and control efforts is wide-ranging, especially for lower and middle-income countries (LMICs), including Malaysia. This paper explores the performance of the col- orectal cancer screening programme in Malaysia for the years 2019 and 2020, This is followed by evidence-based recommendations for building back a better cancer control programme in Malaysia. Malaysia screened a total of 31,529 eligible candidates in 2019 and 42,554 in 2020. A total of 2,668 (8.46%) and 2767 (6.50%) individuals tested positive for the immunochemical faecal occult blood test (iFOBT) in 2019 and 2020 respectively. Of these numbers, only 1454 (54.49%) of those who tested positive underwent colonoscopy in 2019 and this proportion reduced to 1148 (41.48%) in 2020. This analysis also shows a drop in the number of screenings in the second quarter of 2020. This drop coincides with the announcement of Malaysia’s first Movement Control Order. Existing challenges exac- erbated by pandemic restrictions have possibly led to a decreased colonoscopy attendance rate in 2020. To build back a better cancer control programme, better governance, and political will, coupled with improved financing, sustainable partnerships, improved service delivery, and a robust monitoring and evaluation mechanism is vital.