How the neural substrates for detection of paired stimuli are distinct from unpaired stimuli is poorly understood and a fundamental question for understanding the signalling mechanisms for coincidence detection during associative learning. To address this question, we used a neural correlate of eyeblink classical conditioning in an isolated brainstem from the turtle, in which the cranial nerves are directly stimulated in place of using a tone or airpuff. A bidirectional response is activated in <5 min of training, in which phosphorylated 3-phosphoinositide-dependent kinase-1 (p-PDK1) is increased in response to paired and decreased in response to unpaired nerve stimulation and is mediated by the opposing actions of neurotrophin receptors TrkB and p75NTR. Surprisingly, blockade of adenosine 2A (A2A) receptors inhibits both of these responses. Pairing also induces substantially increased surface expression of TrkB that is inhibited by Src family tyrosine kinase and A2A receptor antagonists. Finally, the acquisition of conditioning is blocked by a PDK1 inhibitor. The unique action of A2A receptors to function directly as G proteins and in receptor transactivation to control distinct TrkB and p75NTR signalling pathways allows for convergent activation of PDK1 and protein kinase A during paired stimulation to initiate classical conditioning.