Background Multimorbidity has become one of the main challenges in the recent years for patients, health care providers and the health care systems globally. However, literature describing the burden of multimorbidity in the elderly population, especially longitudinal trends is very limited. Physical activity is recommended as one of the main lifestyle changes in the prevention and management of multiple chronic diseases worldwide; however, the evidence on its association with multimorbidity remains inconclusive. Therefore, we aimed to assess the longitudinal trends of multimorbidity and the association between multimorbidity and physical activity in a nationally representative cohort of the English population aged ≥50 years between 2002 and 2013. Methods We used data on 15,688 core participants from six waves of the English Longitudinal Study of Ageing, with complete information on physical activity. Self-reported physical activity was categorised as inactive, mild, moderate and vigorous levels of physical activity. We calculated the number of morbidities and the prevalence of multimorbidity (more than 2 chronic conditions) between 2002 and 2013 overall and by levels of self-reported physical activity. We estimated the odds ratio (OR) and 95 % confidence intervals (CI) for multimorbidity by each category of physical activity, adjusting for potential confounders. Results There was a progressive decrease over time in the proportion of participants without any chronic conditions (33.9 % in 2002/2003 vs. 26.8 % in 2012/2013). In contrast, the prevalence of multimorbidity steadily increased over time (31.7 % in 2002/2003 vs. 43.1 % in 2012/2013). Compared to the physically inactive group, the OR for multimorbidity was 0.84 (95 % CI 0.78 to 0.91) in mild, 0.61 (95 % CI 0.56 to 0.66) in moderate and 0.45 (95 % CI 0.41 to 0.49) in the vigorous physical activity group. Conclusion This study demonstrated an inverse dose-response association between levels of physical activity and multimorbidity, however, given the increasing prevalence of multimorbidity over time, there is a need to explore causal associations between physical activity and multimorbidity and its impact as a primary prevention strategy to prevent the occurrence of chronic conditions later in life and reduce the burden of multimorbidity. Electronic supplementary material The online version of this article (doi:10.1186/s12966-016-0330-9) contains supplementary material, which is available to authorized users.