In March 2014, Pajuelo was hired as an assistant manager for his former club Universitario.[6] On 1 September 2015, manager Luis Fernando Suárez was fired and Pajuelo took over as a caretaker manager.[7] It only lasted for some days, before Roberto Challe was hired.[8]
Pajuelo left Universitario at the end of 2015, and became the manager of Atlético Torino for the 2016 season.[9] He was fired on 19 May 2016 due to bad results.[10]
In July 2018, he then became the manager of Comerciantes Unidos.[9] He was fired again after two months.[9] In January 2019, he returned to Universitario and was hired as the reserve team manager.[11]