Recently, major progress has been made towards the realisation of the quantum internet to enable a broad range of applications that would be out of reach for classical internet. Most of these applications such as delegated quantum computation require running a secure identification protocol between a low-resource and a high-resource party to provide secure communication. Physical Unclonable Functions (PUFs) have been shown as resource-efficient hardware solutions for providing secure identification schemes in both classical and quantum settings. In this work, we propose two identification protocols based on quantum PUFs (qPUFs) as defined by Arapinis et al. In the first protocol, the low-resource party wishes to prove its identity to the high-resource party and in the second protocol, it is vice versa. Unlike existing identification protocols based on Quantum Read-out PUFs which rely on the security against a specific family of attacks, our protocols provide provable exponential security against any Quantum Polynomial-Time (QPT) adversary with resource-efficient parties. We provide a comprehensive comparison between the two proposed protocols in terms of resources such as quantum memory and computing ability required in both parties as well as the communication overhead between them. A stand-out feature of our second protocol is secure identification of a high-resource party by running a purely classical verification algorithm. This is achieved by delegating quantum operations to the high-resource party and utilising the resulting classical outcomes for identification.