RNAs can fold into heterogeneous structural ensembles populating a complex energy landscape. Structural analysis of RNA loops poses particular challenges and the relationships between their primary sequence, structure, and energy of loops remains enigmatic. We here report the characterisation of the conformational heterogeneity and dynamics of the apical loop in the stem loop 2 motif (s2m) of SARS-CoV-2 (SCoV-2) Delta using a combination of nuclear magnetic resonance spectroscopy (NMR) and molecular dynamics simulations (MD). The apical nonaloop of s2m is flexible and exhibits substantial dynamics, rendering representation of the structure by a single conformation unsuitable. Thus, we report an ensemble of NMR structures in best agreement with SAXS data and weighted MD simulations enabling the representation of the conformational space in the s2m nonaloop and its transient closing 5’-G-U-3’ base pair. This integrated approach is a critical step towards a more complete biophysical characterisation of large RNA apical loops beyond tetra and pentaloops. Our deconvolution of the ensemble into conformations defined by specific interactions and dynamics provides a basis for future ensemble-functional characterisation of this conserved non-coding RNA element and its mutants occurring in variants of concern of SARS-CoV-2.