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 colorectal 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 exacerbated 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.