Microalgae are photosynthetic microorganisms living in marine or freshwater environment. In this study, samples of Chlorella spp. and Nannochloropsis from two different origins were analysed to settle a preliminary characterization of these microorganisms as intermediate energy carriers and their properties compared to a conventional lignocellulosic feedstock (pine chips). Both microalgae samples were characterized in terms of elemental composition (CHONS and P) and thermogravimetric behavior. This was investigated through non-isothermal thermogravimetric analysis in nitrogen atmosphere at heating rate of 15 °C min−1 and temperature up to 800 °C. Solid residues produced at 300 °C and 800 °C from TGA were also analysed to determine the ultimate composition of chars. Activation energy, reaction order and pre-exponential factor were calculated for the single step conversion mechanism of 1 g of Chlorella spp. and compared to literature data on Chlorella protothecoides and Spirulina platensis. Calculated kinetic parameters, given as intervals of several determinations, resulted to be: pre-exponential factor (A) 1.47–1.62E6 min−1, activation energy (E) 7.13–7.92E4 J mol−1, reaction order (n) 1.69–2.41. 1.2 kg of Chlorella spp. was then processed in a newly designed batch pyrolysis pilot reactor, capable of converting up to 1.5 kg h−1 of material, and pyrolysis liquid collected, analysed and compared with a sample of fast pyrolysis from pine chips. This preliminary investigation aimed at carrying out a first characterization of algae oil and optimise the operational aspects of the reactor, tested with the first time with this unconventional feedstock. The algae pyrolysis oil exhibited superior properties as intermediate energy carrier compared to pyrolysis oil from fast pyrolysis of pine chips, in particular higher HHV and carbon content and lower oxygen and water content. These data can potentially be used in the design and modelling of thermochemical conversion processes of microalgae.