This paper examines long-term (more than four solar cycles) temporal and spatial fluctuations in the solar rotation by investigating radio-emission escapes from various layers of the solar atmosphere during the years 1967–2010. The flux modulation approach can also be used to investigate variations in solar rotation, which is a contentious topic in solar physics. This study makes use of a time-series of radio flux data at various frequencies (245–15 400 MHz) obtained at Sagamore Hill Solar Radio Observatory in Massachusetts, USA, and at other observatories from 1967 to 2010. The periodicity present in the temporal variation of the time-series is estimated through a Lomb–Scargle periodogram. The rotation period estimated for five radio emissions (606, 1415, and 2695 MHz from the corona, and 4995 and 8800 MHz from the transition region) through a statistical approach shows continuous temporal and spatial variations throughout the years. The smoothed rotation period shows the presence of periodic ∼22-yr and ∼11-yr components. The 22-yr component could be linked to the reversal of the solar magnetic field (Hale) cycle, while the 11-yr component is most likely related to the sunspot (Schwabe) cycle. In addition to these two components, random components are also prominently present in the analysed data. The cross-correlation between the sunspot number and the rotation period obtained shows a strong correlation with the 11-yr Schwabe and 22-yr Hale cycle. The corona rotates faster or slower than the transition region in different epochs. The alternation of the faster rotation speed between the corona and transition region also follows the 22-yr cycle.