After the 2009-2010 H1N1 pandemic, Switzerland overhauled its 1970 law on epidemics. The reform aimed at improving early detection, surveillance, and preparedness for future outbreaks of infectious diseases. Notably, the law introduced stronger coordination between Federal and Cantonal authorities, better management tools and international cooperation. The new law entered into force in 2016 after a long legislative process. During the process, the law survived a referendum fuelled by concerns about vaccine safety and interference of the pharmaceutical industry. The law was first applied during the COVID-19 pandemic in early 2020. The epicentre of the outbreak in Europe was in Lombardy, a large Italian region adjacent to Switzerland and with strong economic ties with its southern region of Ticino. The first months of pandemic response highlighted three major weaknesses. Firstly, the mechanisms introduced by the new law did not fully succeed in reducing the tension between Cantonal autonomy and central coordination of the pandemic response. Central and Cantonal authorities will need to put in place new rules and arrangements to avoid dangerous delayed responses to foreseeable problems related to the spread of infectious diseases. Secondly, relevant stakeholders excluded from the policymaking process (trade unions, firms, large industries) should be involved to allow the introduction of harsh restrictions when needed, both internally and in relation to cross-border workers.